Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/inputs/xbw Working: n-9-20.cluster.ucsf.bkslab.org:/scratch/xiaobo/323031/xbw-8058115.49 Result: /scratch/xiaobo/323031/xbw-8058115.49 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xbw 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/xbw mkdir: created directory `/scratch/xiaobo/323031' mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49' /scratch/xiaobo/323031/xbw-8058115.49 /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/323031/xbw-8058115.49/working' mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/protonate' Storing results in /scratch/xiaobo/323031/xbw-8058115.49/finished Working in /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 /scratch/xiaobo/323031/xbw-8058115.49/working/protonate /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Using inputs as protomers/tautomers. No processing done 474 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/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Bulk generating 3D conformations all protomers in /scratch/xiaobo/323031/xbw-8058115.49/working/3D mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/323031/xbw-8058115.49/working/protonate/xbw-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 ZINC001300611436 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building' mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001300611436' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001300611436 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC001300611436 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001300611436/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001300611436 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/1 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@]1(C)CN2CCC1CC2) `ZINC001300611436.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001300611436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001300611436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001300611436 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@]1(C)CN2CCC1CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 5, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 17, 17, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 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, 42, 43, 44, 45]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001300611436 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001300611436 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/finished' Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001300611436/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001300611436 Building ZINC001302351108 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351108' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351108 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001302351108 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351108/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351108 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/2 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)Cc2c[nH]nc21) `ZINC001302351108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001302351108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001302351108 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)Cc2c[nH]nc21 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 1, 1, 8, 6, 8, 1, 7, 7, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 5, 1, 1, 1, 5, 5, 5, 17, 17, 17, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 17, 17, 5, 5, 5, 5, 9, 9, 9] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351108 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351108/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351108 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/3 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/3' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)Cc2c[nH]nc21) `ZINC001302351108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001302351108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001302351108 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)Cc2c[nH]nc21 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 1, 1, 8, 6, 8, 1, 7, 7, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 4, 4, 4, 16, 16, 16, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 16, 16, 4, 4, 4, 4, 8, 8, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351108 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001302351108 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351108/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351108/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351108 Building ZINC001302351108 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351108' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351108 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001302351108 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351108/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351108 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 2) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/2: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)Cc2c[nH]nc21) `ZINC001302351108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001302351108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001302351108 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)Cc2c[nH]nc21 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 1, 1, 8, 6, 8, 1, 7, 7, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 5, 1, 1, 1, 5, 5, 5, 17, 17, 17, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 17, 17, 5, 5, 5, 5, 9, 9, 9] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351108 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351108/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351108 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 3) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/3: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)Cc2c[nH]nc21) `ZINC001302351108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001302351108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001302351108 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)Cc2c[nH]nc21 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 1, 1, 8, 6, 8, 1, 7, 7, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 4, 4, 4, 16, 16, 16, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 16, 16, 4, 4, 4, 4, 8, 8, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351108 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001302351108 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351108/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351108/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351108 Building ZINC001302351109 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351109' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001302351109 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351109/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/4 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)Cc2c[nH]nc21) `ZINC001302351109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001302351109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001302351109 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)Cc2c[nH]nc21 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 1, 1, 8, 6, 8, 1, 7, 7, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 5, 5, 5, 17, 17, 17, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 17, 17, 5, 5, 5, 5, 8, 8, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351109/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/5 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/5' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)Cc2c[nH]nc21) `ZINC001302351109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001302351109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001302351109 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)Cc2c[nH]nc21 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 1, 1, 8, 6, 8, 1, 7, 7, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 5, 1, 1, 1, 5, 5, 5, 16, 16, 16, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 16, 16, 5, 5, 5, 5, 9, 9, 9] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001302351109 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351109/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351109/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351109 Building ZINC001302351109 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351109' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001302351109 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351109/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 4) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/4: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)Cc2c[nH]nc21) `ZINC001302351109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001302351109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001302351109 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)Cc2c[nH]nc21 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 1, 1, 8, 6, 8, 1, 7, 7, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 5, 5, 5, 17, 17, 17, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 17, 17, 5, 5, 5, 5, 8, 8, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351109/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 5) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/5: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)Cc2c[nH]nc21) `ZINC001302351109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001302351109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001302351109 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)Cc2c[nH]nc21 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 1, 1, 8, 6, 8, 1, 7, 7, 7, 7, 7, 7, 6, 6, 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, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 5, 1, 1, 1, 5, 5, 5, 16, 16, 16, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 16, 16, 5, 5, 5, 5, 9, 9, 9] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001302351109 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351109/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351109/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302351109 Building ZINC001302750842 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001302750842 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/6 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2) `ZINC001302750842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001302750842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001302750842 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 5, 1, 1, 1, 1, 4, 4, 4, 8, 13, 15, 8, 18, 18, 18, 18, 18, 5, 5, 5, 5, 17, 17, 5, 4, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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, 42]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/7 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/7' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2) `ZINC001302750842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001302750842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001302750842 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 5, 1, 1, 1, 1, 4, 4, 4, 8, 12, 14, 8, 16, 16, 16, 16, 16, 5, 5, 5, 5, 17, 17, 5, 4, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16] 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, 42]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/8 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/8' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2) `ZINC001302750842.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001302750842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001302750842 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 5, 1, 1, 1, 1, 4, 4, 4, 8, 13, 15, 8, 18, 18, 18, 18, 18, 5, 5, 5, 5, 17, 17, 5, 4, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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, 42]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/9 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/9' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2) `ZINC001302750842.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001302750842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001302750842 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 5, 1, 1, 1, 1, 4, 4, 4, 8, 12, 14, 8, 16, 16, 16, 16, 16, 5, 5, 5, 5, 17, 17, 5, 4, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16] 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, 42]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001302750842 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 Building ZINC001302750842 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001302750842 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 6) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/6: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2) `ZINC001302750842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001302750842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001302750842 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 5, 1, 1, 1, 1, 4, 4, 4, 8, 13, 15, 8, 18, 18, 18, 18, 18, 5, 5, 5, 5, 17, 17, 5, 4, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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, 42]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 7) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/7: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2) `ZINC001302750842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001302750842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001302750842 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 5, 1, 1, 1, 1, 4, 4, 4, 8, 12, 14, 8, 16, 16, 16, 16, 16, 5, 5, 5, 5, 17, 17, 5, 4, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16] 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, 42]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 8) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/8: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2) `ZINC001302750842.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001302750842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001302750842 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 5, 1, 1, 1, 1, 4, 4, 4, 8, 13, 15, 8, 18, 18, 18, 18, 18, 5, 5, 5, 5, 17, 17, 5, 4, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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, 42]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 9) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/9: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2) `ZINC001302750842.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001302750842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001302750842 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 5, 1, 1, 1, 1, 4, 4, 4, 8, 12, 14, 8, 16, 16, 16, 16, 16, 5, 5, 5, 5, 17, 17, 5, 4, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16] 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, 42]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001302750842 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 Building ZINC001302750842 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001302750842 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 6) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/6: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2) `ZINC001302750842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001302750842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001302750842 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 5, 1, 1, 1, 1, 4, 4, 4, 8, 13, 15, 8, 18, 18, 18, 18, 18, 5, 5, 5, 5, 17, 17, 5, 4, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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, 42]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 7) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/7: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2) `ZINC001302750842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001302750842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001302750842 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 5, 1, 1, 1, 1, 4, 4, 4, 8, 12, 14, 8, 16, 16, 16, 16, 16, 5, 5, 5, 5, 17, 17, 5, 4, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16] 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, 42]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 8) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/8: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2) `ZINC001302750842.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001302750842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001302750842 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 5, 1, 1, 1, 1, 4, 4, 4, 8, 13, 15, 8, 18, 18, 18, 18, 18, 5, 5, 5, 5, 17, 17, 5, 4, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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, 42]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 9) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/9: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2) `ZINC001302750842.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001302750842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001302750842 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 5, 1, 1, 1, 1, 4, 4, 4, 8, 12, 14, 8, 16, 16, 16, 16, 16, 5, 5, 5, 5, 17, 17, 5, 4, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16] 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, 42]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001302750842 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 Building ZINC001302750842 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001302750842 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 6) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/6: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2) `ZINC001302750842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001302750842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001302750842 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 5, 1, 1, 1, 1, 4, 4, 4, 8, 13, 15, 8, 18, 18, 18, 18, 18, 5, 5, 5, 5, 17, 17, 5, 4, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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, 42]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 7) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/7: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2) `ZINC001302750842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001302750842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001302750842 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 5, 1, 1, 1, 1, 4, 4, 4, 8, 12, 14, 8, 16, 16, 16, 16, 16, 5, 5, 5, 5, 17, 17, 5, 4, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16] 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, 42]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 8) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/8: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2) `ZINC001302750842.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001302750842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001302750842 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 5, 1, 1, 1, 1, 4, 4, 4, 8, 13, 15, 8, 18, 18, 18, 18, 18, 5, 5, 5, 5, 17, 17, 5, 4, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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, 42]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 9) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/9: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2) `ZINC001302750842.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001302750842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001302750842 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)Nc1cc2n(n1)CCN(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 5, 1, 1, 1, 1, 4, 4, 4, 8, 12, 14, 8, 16, 16, 16, 16, 16, 5, 5, 5, 5, 17, 17, 5, 4, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16] 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, 42]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001302750842 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302750842 Building ZINC001302863857 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863857' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863857 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001302863857 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863857/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863857 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/10 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001302863857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001302863857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001302863857 none CNC(=O)NC[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 22, 12, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 1, 1, 1, 5, 5, 5, 5, 11, 11, 11, 5, 30, 30, 30, 30, 22, 12, 12, 4, 4, 4, 4, 4, 4, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 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, 46, 47, 48, 49]) total number of confs: 145 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863857 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863857/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863857 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/11 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/11' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001302863857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001302863857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001302863857 none CNC(=O)NC[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 20, 22, 11, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 16, 16, 16, 6, 30, 30, 30, 30, 20, 11, 11, 4, 4, 4, 4, 4, 4, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 159 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863857 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001302863857 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863857/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863857/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863857 Building ZINC001302863857 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863857' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863857 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001302863857 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863857/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863857 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 10) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/10: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001302863857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001302863857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001302863857 none CNC(=O)NC[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 22, 12, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 1, 1, 1, 5, 5, 5, 5, 11, 11, 11, 5, 30, 30, 30, 30, 22, 12, 12, 4, 4, 4, 4, 4, 4, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 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, 46, 47, 48, 49]) total number of confs: 145 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863857 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863857/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863857 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 11) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/11: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001302863857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001302863857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001302863857 none CNC(=O)NC[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 20, 22, 11, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 16, 16, 16, 6, 30, 30, 30, 30, 20, 11, 11, 4, 4, 4, 4, 4, 4, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 159 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863857 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001302863857 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863857/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863857/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863857 Building ZINC001302863858 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863858' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863858 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001302863858 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863858/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863858 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/12 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001302863858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001302863858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001302863858 none CNC(=O)NC[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 19, 10, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 17, 17, 17, 6, 26, 26, 26, 26, 18, 10, 10, 3, 3, 3, 3, 3, 3, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 150 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863858 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863858/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863858 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/13 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/13' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001302863858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001302863858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001302863858 none CNC(=O)NC[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 23, 23, 23, 12, 5, 5, 5, 5, 5, 5, 5, 5, 2, 5, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 30, 30, 30, 30, 23, 12, 12, 5, 5, 5, 5, 5, 5, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 139 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863858 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001302863858 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863858/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863858/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863858 Building ZINC001302863858 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863858' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863858 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001302863858 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863858/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863858 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 12) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/12: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001302863858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001302863858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001302863858 none CNC(=O)NC[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 19, 10, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 17, 17, 17, 6, 26, 26, 26, 26, 18, 10, 10, 3, 3, 3, 3, 3, 3, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 150 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863858 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863858/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863858 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 13) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/13: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001302863858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001302863858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001302863858 none CNC(=O)NC[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 23, 23, 23, 12, 5, 5, 5, 5, 5, 5, 5, 5, 2, 5, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 30, 30, 30, 30, 23, 12, 12, 5, 5, 5, 5, 5, 5, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 139 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863858 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001302863858 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863858/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863858/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302863858 Building ZINC001302943173 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302943173' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302943173 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001302943173 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302943173/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302943173 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/14 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1cc(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c(O)nc1=O) `ZINC001302943173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001302943173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302943173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001302943173 none COCCn1cc(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 33, 22, 22, 22, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 22, 22, 22, 22, 22, 43, 43, 43, 43, 43, 33, 33, 22, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 66] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302943173 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302943173/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302943173 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/15 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/15' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1cc(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c(O)nc1=O) `ZINC001302943173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001302943173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302943173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001302943173 none COCCn1cc(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 43, 32, 22, 22, 22, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 22, 22, 22, 22, 22, 44, 44, 44, 43, 43, 32, 32, 22, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 66] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302943173 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001302943173 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302943173/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302943173/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302943173 Building ZINC001302943173 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302943173' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302943173 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001302943173 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302943173/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302943173 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 14) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1cc(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c(O)nc1=O) `ZINC001302943173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001302943173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302943173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001302943173 none COCCn1cc(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 33, 22, 22, 22, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 22, 22, 22, 22, 22, 43, 43, 43, 43, 43, 33, 33, 22, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 66] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302943173 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302943173/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302943173 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 15) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1cc(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c(O)nc1=O) `ZINC001302943173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001302943173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302943173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001302943173 none COCCn1cc(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c(O)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 43, 32, 22, 22, 22, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 22, 22, 22, 22, 22, 44, 44, 44, 43, 43, 32, 32, 22, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 66] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302943173 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001302943173 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302943173/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302943173/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001302943173 Building ZINC001303025325 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001303025325' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001303025325 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303025325 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001303025325/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001303025325 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/16 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(C)(N2CCC2)CC1) `ZINC001303025325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303025325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001303025325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001303025325 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(C)(N2CCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 2, 1, 1, 1, 2, 4, 6, 12, 12, 12, 12, 14, 19, 19, 16, 12, 12, 2, 2, 2, 2, 7, 7, 2, 12, 12, 12, 12, 12, 12, 12, 19, 19, 19, 19, 19, 19, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 71 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001303025325 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001303025325/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001303025325 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/17 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/17' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(C)(N2CCC2)CC1) `ZINC001303025325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303025325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001303025325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001303025325 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(C)(N2CCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 2, 1, 1, 1, 2, 4, 6, 11, 11, 11, 11, 11, 14, 14, 11, 11, 11, 2, 2, 2, 2, 7, 7, 2, 11, 11, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 11, 11, 11, 11] 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: 63 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001303025325 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001303025325 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001303025325/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001303025325/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001303025325 Building ZINC001303025325 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001303025325' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001303025325 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001303025325 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001303025325/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001303025325 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 16) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/16: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(C)(N2CCC2)CC1) `ZINC001303025325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001303025325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001303025325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001303025325 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(C)(N2CCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 2, 1, 1, 1, 2, 4, 6, 12, 12, 12, 12, 14, 19, 19, 16, 12, 12, 2, 2, 2, 2, 7, 7, 2, 12, 12, 12, 12, 12, 12, 12, 19, 19, 19, 19, 19, 19, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 71 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001303025325 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001303025325/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001303025325 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 17) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/17: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(C)(N2CCC2)CC1) `ZINC001303025325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001303025325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001303025325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001303025325 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(C)(N2CCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 2, 1, 1, 1, 2, 4, 6, 11, 11, 11, 11, 11, 14, 14, 11, 11, 11, 2, 2, 2, 2, 7, 7, 2, 11, 11, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 11, 11, 11, 11] 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: 63 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001303025325 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001303025325 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001303025325/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001303025325/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001303025325 Building ZINC001318190828 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190828' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190828 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001318190828 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190828/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190828 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/18 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCc2cccc([C@]3(C)NC(=O)NC3=O)c2)cn1) `ZINC001318190828.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001318190828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001318190828 none Cn1cc([C@]([O-])([SiH3])C(=O)NCc2cccc([C@]3(C)NC(=O)NC3=O)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 8, 1, 11, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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: [4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 15, 30, 30, 30, 30, 30, 47, 47, 47, 47, 47, 47, 47, 30, 4, 4, 4, 4, 4, 4, 3, 15, 15, 30, 30, 30, 47, 47, 47, 47, 47, 30, 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190828 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190828/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190828 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/19 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/19' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2cccc([C@]3(C)NC(=O)NC3=O)c2)cn1) `ZINC001318190828.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001318190828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190828/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001318190828 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2cccc([C@]3(C)NC(=O)NC3=O)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 8, 1, 11, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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: [4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 14, 28, 28, 25, 28, 28, 45, 45, 45, 45, 45, 45, 45, 28, 4, 4, 4, 4, 4, 4, 2, 14, 14, 28, 28, 28, 45, 45, 45, 45, 45, 28, 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]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190828 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001318190828 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190828/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190828/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190828 Building ZINC001318190828 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190828' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190828 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001318190828 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190828/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190828 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 18) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/18: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCc2cccc([C@]3(C)NC(=O)NC3=O)c2)cn1) `ZINC001318190828.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001318190828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001318190828 none Cn1cc([C@]([O-])([SiH3])C(=O)NCc2cccc([C@]3(C)NC(=O)NC3=O)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 8, 1, 11, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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: [4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 15, 30, 30, 30, 30, 30, 47, 47, 47, 47, 47, 47, 47, 30, 4, 4, 4, 4, 4, 4, 3, 15, 15, 30, 30, 30, 47, 47, 47, 47, 47, 30, 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190828 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190828/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190828 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 19) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/19: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2cccc([C@]3(C)NC(=O)NC3=O)c2)cn1) `ZINC001318190828.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001318190828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190828/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001318190828 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2cccc([C@]3(C)NC(=O)NC3=O)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 8, 1, 11, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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: [4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 14, 28, 28, 25, 28, 28, 45, 45, 45, 45, 45, 45, 45, 28, 4, 4, 4, 4, 4, 4, 2, 14, 14, 28, 28, 28, 45, 45, 45, 45, 45, 28, 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]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190828 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001318190828 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190828/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190828/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190828 Building ZINC001318190829 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190829' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190829 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001318190829 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190829/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190829 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/20 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCc2cccc([C@@]3(C)NC(=O)NC3=O)c2)cn1) `ZINC001318190829.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001318190829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001318190829 none Cn1cc([C@]([O-])([SiH3])C(=O)NCc2cccc([C@@]3(C)NC(=O)NC3=O)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 8, 1, 11, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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: [4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 14, 29, 29, 21, 29, 29, 44, 44, 44, 44, 44, 44, 44, 27, 4, 4, 4, 4, 4, 4, 2, 14, 14, 29, 29, 29, 44, 44, 44, 44, 44, 29, 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]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190829 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190829/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190829 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/21 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/21' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2cccc([C@@]3(C)NC(=O)NC3=O)c2)cn1) `ZINC001318190829.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001318190829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190829/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001318190829 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2cccc([C@@]3(C)NC(=O)NC3=O)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 8, 1, 11, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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: [4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 15, 29, 29, 29, 29, 29, 46, 46, 46, 46, 46, 46, 46, 29, 4, 4, 4, 4, 4, 4, 3, 15, 15, 29, 29, 29, 46, 46, 46, 46, 46, 29, 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190829 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001318190829 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190829/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190829/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190829 Building ZINC001318190829 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190829' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190829 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001318190829 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190829/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190829 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 20) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/20: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCc2cccc([C@@]3(C)NC(=O)NC3=O)c2)cn1) `ZINC001318190829.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001318190829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001318190829 none Cn1cc([C@]([O-])([SiH3])C(=O)NCc2cccc([C@@]3(C)NC(=O)NC3=O)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 8, 1, 11, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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: [4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 14, 29, 29, 21, 29, 29, 44, 44, 44, 44, 44, 44, 44, 27, 4, 4, 4, 4, 4, 4, 2, 14, 14, 29, 29, 29, 44, 44, 44, 44, 44, 29, 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]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190829 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190829/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190829 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 21) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/21: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2cccc([C@@]3(C)NC(=O)NC3=O)c2)cn1) `ZINC001318190829.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001318190829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190829/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001318190829 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2cccc([C@@]3(C)NC(=O)NC3=O)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 8, 1, 11, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 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: [4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 15, 29, 29, 29, 29, 29, 46, 46, 46, 46, 46, 46, 46, 29, 4, 4, 4, 4, 4, 4, 3, 15, 15, 29, 29, 29, 46, 46, 46, 46, 46, 29, 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190829 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001318190829 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190829/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190829/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001318190829 Building ZINC001320887857 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320887857' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320887857 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001320887857 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320887857/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320887857 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/22 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC2(CC(=O)OC)CCS(=O)(=O)CC2)cn1) `ZINC001320887857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001320887857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320887857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001320887857 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC2(CC(=O)OC)CCS(=O)(=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 12, 5, 5, 5, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 12, 16, 16, 16, 4, 4, 4, 4, 4, 4, 4, 5, 5, 10, 10, 10, 10, 10, 5, 2, 12, 12, 16, 16, 16, 4, 4, 4, 4, 4, 4, 4, 4, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320887857 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320887857/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320887857 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/23 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/23' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC2(CC(=O)OC)CCS(=O)(=O)CC2)cn1) `ZINC001320887857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001320887857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320887857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001320887857 none CCn1cc([C@]([O-])([SiH3])C(=O)NC2(CC(=O)OC)CCS(=O)(=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 12, 5, 5, 5, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 12, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 5, 5, 10, 10, 10, 10, 10, 5, 2, 12, 12, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320887857 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001320887857 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320887857/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320887857/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320887857 Building ZINC001320887857 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320887857' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320887857 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001320887857 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320887857/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320887857 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 22) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/22: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC2(CC(=O)OC)CCS(=O)(=O)CC2)cn1) `ZINC001320887857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001320887857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320887857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001320887857 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC2(CC(=O)OC)CCS(=O)(=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 12, 5, 5, 5, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 12, 16, 16, 16, 4, 4, 4, 4, 4, 4, 4, 5, 5, 10, 10, 10, 10, 10, 5, 2, 12, 12, 16, 16, 16, 4, 4, 4, 4, 4, 4, 4, 4, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320887857 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320887857/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320887857 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 23) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/23: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC2(CC(=O)OC)CCS(=O)(=O)CC2)cn1) `ZINC001320887857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001320887857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320887857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001320887857 none CCn1cc([C@]([O-])([SiH3])C(=O)NC2(CC(=O)OC)CCS(=O)(=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 12, 5, 5, 5, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 12, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 5, 5, 10, 10, 10, 10, 10, 5, 2, 12, 12, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320887857 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001320887857 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320887857/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320887857/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320887857 Building ZINC001320992274 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992274' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992274 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001320992274 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992274/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992274 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/24 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)N[C@@H]1CCS(=O)(=O)C1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001320992274.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001320992274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001320992274 none CN(CC(=O)N[C@@H]1CCS(=O)(=O)C1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 22, 22, 32, 50, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 11, 11, 22, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992274 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992274/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992274 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/25 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/25' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)N[C@@H]1CCS(=O)(=O)C1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001320992274.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001320992274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992274/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001320992274 none CN(CC(=O)N[C@@H]1CCS(=O)(=O)C1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 22, 22, 30, 50, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 11, 11, 22, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992274 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001320992274 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992274/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992274/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992274 Building ZINC001320992274 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992274' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992274 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001320992274 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992274/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992274 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 24) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/24: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)N[C@@H]1CCS(=O)(=O)C1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001320992274.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001320992274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001320992274 none CN(CC(=O)N[C@@H]1CCS(=O)(=O)C1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 22, 22, 32, 50, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 11, 11, 22, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992274 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992274/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992274 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 25) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/25: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)N[C@@H]1CCS(=O)(=O)C1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001320992274.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001320992274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992274/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001320992274 none CN(CC(=O)N[C@@H]1CCS(=O)(=O)C1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 22, 22, 30, 50, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 11, 11, 22, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992274 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001320992274 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992274/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992274/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992274 Building ZINC001320992276 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992276' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992276 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001320992276 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992276/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992276 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/26 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)N[C@H]1CCS(=O)(=O)C1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001320992276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001320992276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001320992276 none CN(CC(=O)N[C@H]1CCS(=O)(=O)C1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 22, 22, 30, 50, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 11, 11, 22, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 163 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992276 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992276/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992276 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/27 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/27' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)N[C@H]1CCS(=O)(=O)C1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001320992276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001320992276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001320992276 none CN(CC(=O)N[C@H]1CCS(=O)(=O)C1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 20, 20, 30, 50, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 10, 10, 20, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992276 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001320992276 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992276/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992276/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992276 Building ZINC001320992276 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992276' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992276 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001320992276 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992276/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992276 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 26) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/26: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)N[C@H]1CCS(=O)(=O)C1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001320992276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001320992276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001320992276 none CN(CC(=O)N[C@H]1CCS(=O)(=O)C1)C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 22, 22, 30, 50, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 11, 11, 22, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 163 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992276 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992276/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992276 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 27) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/27: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)N[C@H]1CCS(=O)(=O)C1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001320992276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001320992276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001320992276 none CN(CC(=O)N[C@H]1CCS(=O)(=O)C1)C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 20, 20, 30, 50, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 6, 6, 10, 10, 20, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992276 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001320992276 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992276/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992276/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001320992276 Building ZINC001324628204 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001324628204' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001324628204 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001324628204 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001324628204/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001324628204 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/28 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/28' -> `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)Nc1nc(C)n(C)c1C(=O)NCCO) `ZINC001324628204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001324628204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001324628204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001324628204 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc(C)n(C)c1C(=O)NCCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 8, 5, 1, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 37, 41, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 13, 37, 37, 41, 41, 123] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 284 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001324628204 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001324628204/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001324628204 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/29 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/29' -> `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)Nc1nc(C)n(C)c1C(=O)NCCO) `ZINC001324628204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001324628204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001324628204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001324628204 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc(C)n(C)c1C(=O)NCCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 8, 5, 1, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 36, 41, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 13, 36, 36, 41, 41, 123] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 287 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001324628204 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001324628204 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001324628204/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001324628204/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001324628204 Building ZINC001324628204 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001324628204' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001324628204 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001324628204 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001324628204/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001324628204 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 28) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/28: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc(C)n(C)c1C(=O)NCCO) `ZINC001324628204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001324628204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001324628204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001324628204 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc(C)n(C)c1C(=O)NCCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 8, 5, 1, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 37, 41, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 13, 37, 37, 41, 41, 123] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 284 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001324628204 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001324628204/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001324628204 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 29) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/29: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc(C)n(C)c1C(=O)NCCO) `ZINC001324628204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001324628204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001324628204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001324628204 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc(C)n(C)c1C(=O)NCCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 8, 5, 1, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 36, 41, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 13, 36, 36, 41, 41, 123] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 287 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001324628204 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001324628204 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001324628204/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001324628204/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001324628204 Building ZINC001326069945 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001326069945' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001326069945 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001326069945 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001326069945/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001326069945 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/30 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC1(NC(=O)[C@]([O-])([SiH3])c2cccn2C)CCS(=O)(=O)CC1) `ZINC001326069945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001326069945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001326069945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001326069945 none COC(=O)CC1(NC(=O)[C@]([O-])([SiH3])c2cccn2C)CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 35, 43, 12, 8, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 43, 43, 43, 35, 35, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001326069945 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001326069945/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001326069945 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/31 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/31' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC1(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)CCS(=O)(=O)CC1) `ZINC001326069945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001326069945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001326069945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001326069945 none COC(=O)CC1(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 36, 42, 14, 8, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 42, 42, 42, 36, 36, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001326069945 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001326069945 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001326069945/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001326069945/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001326069945 Building ZINC001326069945 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001326069945' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001326069945 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001326069945 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001326069945/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001326069945 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 30) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/30: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC1(NC(=O)[C@]([O-])([SiH3])c2cccn2C)CCS(=O)(=O)CC1) `ZINC001326069945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001326069945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001326069945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001326069945 none COC(=O)CC1(NC(=O)[C@]([O-])([SiH3])c2cccn2C)CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 35, 43, 12, 8, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 43, 43, 43, 35, 35, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001326069945 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001326069945/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001326069945 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 31) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/31: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC1(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)CCS(=O)(=O)CC1) `ZINC001326069945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001326069945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001326069945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001326069945 none COC(=O)CC1(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 36, 42, 14, 8, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 42, 42, 42, 36, 36, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001326069945 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001326069945 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001326069945/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001326069945/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001326069945 Building ZINC001327988571 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001327988571' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001327988571 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001327988571 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001327988571/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001327988571 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/32 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCC[C@@H](C1)C2O) `ZINC001327988571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001327988571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001327988571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001327988571 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCC[C@@H](C1)C2O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 16, 16, 16, 4, 1, 1, 1, 1, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 16, 16, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 24] 150 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, 42, 43, 44]) total number of confs: 93 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001327988571 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001327988571/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001327988571 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/33 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/33' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCC[C@@H](C1)C2O) `ZINC001327988571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001327988571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001327988571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001327988571 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCC[C@@H](C1)C2O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 22, 22, 22, 6, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 22, 22, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 21] 150 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, 42, 43, 44]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001327988571 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001327988571 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001327988571/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001327988571/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001327988571 Building ZINC001327988571 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001327988571' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001327988571 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001327988571 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001327988571/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001327988571 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 32) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/32: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCC[C@@H](C1)C2O) `ZINC001327988571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001327988571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001327988571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001327988571 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCC[C@@H](C1)C2O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 16, 16, 16, 4, 1, 1, 1, 1, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 16, 16, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 24] 150 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, 42, 43, 44]) total number of confs: 93 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001327988571 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001327988571/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001327988571 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 33) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/33: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCC[C@@H](C1)C2O) `ZINC001327988571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001327988571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001327988571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001327988571 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCC[C@@H](C1)C2O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 22, 22, 22, 6, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 22, 22, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 21] 150 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, 42, 43, 44]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001327988571 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001327988571 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001327988571/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001327988571/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001327988571 Building ZINC001328317205 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317205' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317205 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001328317205 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317205/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317205 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/34 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCc2nc[nH]c2C1) `ZINC001328317205.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001328317205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001328317205 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCc2nc[nH]c2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 8, 1, 8, 6, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 13, 4, 1, 1, 1, 1, 4, 4, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 13, 13, 4, 4, 16, 16, 16, 16, 16, 16, 16] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317205 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317205/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317205 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/35 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/35' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCc2nc[nH]c2C1) `ZINC001328317205.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001328317205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317205/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001328317205 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCc2nc[nH]c2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 8, 1, 8, 6, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 12, 12, 5, 1, 1, 1, 1, 3, 3, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 12, 12, 5, 3, 15, 15, 15, 15, 15, 15, 15] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317205 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001328317205 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317205/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317205/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317205 Building ZINC001328317205 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317205' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317205 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001328317205 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317205/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317205 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 34) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/34: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCc2nc[nH]c2C1) `ZINC001328317205.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001328317205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001328317205 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCc2nc[nH]c2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 8, 1, 8, 6, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 13, 4, 1, 1, 1, 1, 4, 4, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 13, 13, 4, 4, 16, 16, 16, 16, 16, 16, 16] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317205 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317205/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317205 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 35) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/35: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCc2nc[nH]c2C1) `ZINC001328317205.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001328317205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317205/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001328317205 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCc2nc[nH]c2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 8, 1, 8, 6, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 12, 12, 5, 1, 1, 1, 1, 3, 3, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 12, 12, 5, 3, 15, 15, 15, 15, 15, 15, 15] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317205 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001328317205 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317205/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317205/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317205 Building ZINC001328317206 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317206' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317206 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001328317206 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317206/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317206 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/36 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCc2nc[nH]c2C1) `ZINC001328317206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001328317206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001328317206 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCc2nc[nH]c2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 8, 1, 8, 6, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 12, 12, 5, 1, 1, 1, 1, 3, 3, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 12, 12, 5, 3, 15, 15, 15, 15, 15, 15, 15] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317206 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317206/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317206 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/37 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/37' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCc2nc[nH]c2C1) `ZINC001328317206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001328317206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001328317206 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCc2nc[nH]c2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 8, 1, 8, 6, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 13, 4, 1, 1, 1, 1, 4, 4, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 13, 13, 4, 4, 16, 16, 16, 16, 16, 16, 16] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317206 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001328317206 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317206/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317206/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317206 Building ZINC001328317206 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317206' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317206 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001328317206 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317206/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317206 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 36) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/36: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCc2nc[nH]c2C1) `ZINC001328317206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001328317206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001328317206 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCc2nc[nH]c2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 8, 1, 8, 6, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 12, 12, 5, 1, 1, 1, 1, 3, 3, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 12, 12, 5, 3, 15, 15, 15, 15, 15, 15, 15] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317206 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317206/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317206 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 37) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/37: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCc2nc[nH]c2C1) `ZINC001328317206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001328317206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001328317206 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCc2nc[nH]c2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 8, 1, 8, 6, 1, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 13, 4, 1, 1, 1, 1, 4, 4, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4, 13, 13, 4, 4, 16, 16, 16, 16, 16, 16, 16] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317206 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001328317206 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317206/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317206/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328317206 Building ZINC001328422964 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328422964' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328422964 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001328422964 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328422964/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328422964 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/38 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncc(CCNC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n1) `ZINC001328422964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001328422964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328422964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001328422964 none Cc1cncc(CCNC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', '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, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 6, 6, 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, 21, 21, 21, 21, 14, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 21, 21, 21, 21, 21, 21, 14, 14, 10, 10, 2, 2, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328422964 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328422964/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328422964 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/39 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/39' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncc(CCNC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n1) `ZINC001328422964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001328422964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328422964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001328422964 none Cc1cncc(CCNC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', '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, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 6, 6, 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, 21, 21, 21, 21, 14, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 21, 21, 21, 21, 21, 21, 14, 14, 10, 10, 2, 3, 6, 6, 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, 40]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328422964 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001328422964 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328422964/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328422964/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328422964 Building ZINC001328422964 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328422964' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328422964 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001328422964 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328422964/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328422964 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 38) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/38: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncc(CCNC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n1) `ZINC001328422964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001328422964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328422964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001328422964 none Cc1cncc(CCNC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', '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, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 6, 6, 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, 21, 21, 21, 21, 14, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 21, 21, 21, 21, 21, 21, 14, 14, 10, 10, 2, 2, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328422964 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328422964/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328422964 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 39) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/39: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncc(CCNC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n1) `ZINC001328422964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001328422964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328422964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001328422964 none Cc1cncc(CCNC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', '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, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 6, 6, 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, 21, 21, 21, 21, 14, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 21, 21, 21, 21, 21, 21, 14, 14, 10, 10, 2, 3, 6, 6, 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, 40]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328422964 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001328422964 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328422964/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328422964/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328422964 Building ZINC001328540541 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328540541' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328540541 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001328540541 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328540541/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328540541 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/40 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2cnc[nH]2)CC1) `ZINC001328540541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001328540541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328540541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001328540541 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2cnc[nH]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 1, 8, 6, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 2, 1, 1, 1, 1, 4, 8, 11, 11, 11, 11, 17, 17, 17, 17, 17, 11, 11, 2, 2, 2, 2, 7, 7, 2, 11, 11, 11, 11, 11, 17, 17, 11, 11, 11, 11] 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, 42, 43]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328540541 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328540541/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328540541 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/41 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/41' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(c2cnc[nH]2)CC1) `ZINC001328540541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001328540541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328540541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001328540541 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(c2cnc[nH]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 1, 8, 6, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 4, 8, 12, 12, 12, 12, 22, 22, 22, 22, 22, 12, 12, 2, 2, 2, 2, 5, 5, 2, 12, 12, 12, 12, 12, 22, 22, 12, 12, 12, 12] 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, 42, 43]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328540541 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001328540541 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328540541/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328540541/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328540541 Building ZINC001328540541 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328540541' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328540541 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001328540541 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328540541/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328540541 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 40) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/40: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2cnc[nH]2)CC1) `ZINC001328540541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001328540541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328540541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001328540541 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(c2cnc[nH]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 1, 8, 6, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 2, 1, 1, 1, 1, 4, 8, 11, 11, 11, 11, 17, 17, 17, 17, 17, 11, 11, 2, 2, 2, 2, 7, 7, 2, 11, 11, 11, 11, 11, 17, 17, 11, 11, 11, 11] 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, 42, 43]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328540541 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328540541/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328540541 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 41) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/41: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(c2cnc[nH]2)CC1) `ZINC001328540541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001328540541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328540541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001328540541 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(c2cnc[nH]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 8, 1, 8, 6, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 4, 8, 12, 12, 12, 12, 22, 22, 22, 22, 22, 12, 12, 2, 2, 2, 2, 5, 5, 2, 12, 12, 12, 12, 12, 22, 22, 12, 12, 12, 12] 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, 42, 43]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328540541 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001328540541 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328540541/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328540541/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328540541 Building ZINC001328725549 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725549' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725549 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001328725549 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725549/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725549 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/42 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@](O)(C(F)F)C1) `ZINC001328725549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001328725549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001328725549 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@](O)(C(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 7, 2, 1, 1, 1, 1, 2, 4, 11, 11, 11, 11, 11, 18, 18, 11, 2, 2, 2, 2, 7, 7, 2, 11, 11, 11, 11, 33, 18, 11, 11] 150 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725549 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725549/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725549 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/43 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/43' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@](O)(C(F)F)C1) `ZINC001328725549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001328725549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001328725549 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@](O)(C(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 1, 2, 4, 9, 9, 9, 9, 9, 15, 15, 9, 2, 2, 2, 2, 8, 8, 2, 9, 9, 9, 9, 27, 15, 9, 9] 150 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725549 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001328725549 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725549/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725549/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725549 Building ZINC001328725549 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725549' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725549 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001328725549 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725549/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725549 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 42) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/42: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@](O)(C(F)F)C1) `ZINC001328725549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001328725549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001328725549 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@](O)(C(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 7, 2, 1, 1, 1, 1, 2, 4, 11, 11, 11, 11, 11, 18, 18, 11, 2, 2, 2, 2, 7, 7, 2, 11, 11, 11, 11, 33, 18, 11, 11] 150 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725549 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725549/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725549 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 43) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/43: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@](O)(C(F)F)C1) `ZINC001328725549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001328725549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001328725549 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@](O)(C(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 1, 2, 4, 9, 9, 9, 9, 9, 15, 15, 9, 2, 2, 2, 2, 8, 8, 2, 9, 9, 9, 9, 27, 15, 9, 9] 150 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725549 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001328725549 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725549/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725549/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725549 Building ZINC001328725551 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725551' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725551 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001328725551 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725551/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725551 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/44 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@](O)(C(F)F)C1) `ZINC001328725551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001328725551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001328725551 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@](O)(C(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 1, 2, 4, 10, 10, 10, 10, 10, 16, 16, 10, 2, 2, 2, 2, 8, 8, 2, 10, 10, 10, 10, 30, 16, 10, 10] 150 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725551 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725551/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725551 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/45 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/45' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@](O)(C(F)F)C1) `ZINC001328725551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001328725551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001328725551 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@](O)(C(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 1, 2, 4, 9, 9, 9, 9, 9, 12, 12, 9, 2, 2, 2, 2, 8, 8, 2, 9, 9, 9, 9, 27, 12, 9, 9] 150 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725551 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001328725551 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725551/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725551/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725551 Building ZINC001328725551 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725551' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725551 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001328725551 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725551/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725551 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 44) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/44: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@](O)(C(F)F)C1) `ZINC001328725551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001328725551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001328725551 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@](O)(C(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 1, 2, 4, 10, 10, 10, 10, 10, 16, 16, 10, 2, 2, 2, 2, 8, 8, 2, 10, 10, 10, 10, 30, 16, 10, 10] 150 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725551 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725551/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725551 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 45) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/45: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@](O)(C(F)F)C1) `ZINC001328725551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001328725551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001328725551 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@](O)(C(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 1, 2, 4, 9, 9, 9, 9, 9, 12, 12, 9, 2, 2, 2, 2, 8, 8, 2, 9, 9, 9, 9, 27, 12, 9, 9] 150 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725551 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001328725551 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725551/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725551/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001328725551 Building ZINC001329962938 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001329962938' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001329962938 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001329962938 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001329962938/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001329962938 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/46 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCCc2n[nH]cc2C1) `ZINC001329962938.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001329962938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001329962938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001329962938 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCCc2n[nH]cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 8, 6, 1, 1, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 2, 1, 1, 1, 2, 2, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 7, 7, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001329962938 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001329962938/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001329962938 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/47 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/47' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCCc2n[nH]cc2C1) `ZINC001329962938.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001329962938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001329962938/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001329962938 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCCc2n[nH]cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 8, 6, 1, 1, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 10, 3, 1, 1, 1, 2, 4, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 10, 10, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 53 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001329962938 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001329962938 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001329962938/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001329962938/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001329962938 Building ZINC001329962938 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001329962938' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001329962938 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001329962938 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001329962938/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001329962938 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 46) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/46: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCCc2n[nH]cc2C1) `ZINC001329962938.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001329962938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001329962938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001329962938 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCCc2n[nH]cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 8, 6, 1, 1, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 2, 1, 1, 1, 2, 2, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 7, 7, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001329962938 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001329962938/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001329962938 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 47) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/47: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCCc2n[nH]cc2C1) `ZINC001329962938.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001329962938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001329962938/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001329962938 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCCc2n[nH]cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 8, 6, 1, 1, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 10, 3, 1, 1, 1, 2, 4, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 10, 10, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 53 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001329962938 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001329962938 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001329962938/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001329962938/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001329962938 Building ZINC001330149170 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330149170' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330149170 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001330149170 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330149170/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330149170 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/48 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/48' -> `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(NS(N)(=O)=O)CC2)cn1) `ZINC001330149170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001330149170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330149170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001330149170 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC(NS(N)(=O)=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 14, 8, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 5, 18, 29, 29, 29, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 18, 29, 29, 5, 5, 5, 5, 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]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330149170 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330149170/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330149170 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/49 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/49' -> `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(NS(N)(=O)=O)CC2)cn1) `ZINC001330149170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001330149170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330149170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001330149170 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC(NS(N)(=O)=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 14, 8, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 11, 6, 6, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 15, 28, 28, 28, 4, 4, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 4, 4, 4, 4, 4, 15, 28, 28, 4, 4, 4, 4, 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: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330149170 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001330149170 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330149170/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330149170/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330149170 Building ZINC001330149170 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330149170' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330149170 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001330149170 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330149170/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330149170 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 48) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/48: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC(NS(N)(=O)=O)CC2)cn1) `ZINC001330149170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001330149170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330149170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001330149170 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC(NS(N)(=O)=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 14, 8, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 5, 18, 29, 29, 29, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 18, 29, 29, 5, 5, 5, 5, 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]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330149170 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330149170/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330149170 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 49) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/49: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC(NS(N)(=O)=O)CC2)cn1) `ZINC001330149170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001330149170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330149170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001330149170 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC(NS(N)(=O)=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 14, 8, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 11, 6, 6, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 15, 28, 28, 28, 4, 4, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 4, 4, 4, 4, 4, 15, 28, 28, 4, 4, 4, 4, 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: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330149170 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001330149170 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330149170/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330149170/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330149170 Building ZINC001330720507 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330720507' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330720507 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001330720507 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330720507/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330720507 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/50 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n(C)n1) `ZINC001330720507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001330720507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330720507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001330720507 none COCCc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 23, 23, 9, 9, 9, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 9, 9, 9, 24, 24, 24, 23, 23, 23, 23, 9, 5, 1, 4, 4, 1, 1, 1, 1, 9, 9, 9] 50 rigid atoms, others: [34, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 40, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 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/323031/xbw-8058115.49/working/building/ZINC001330720507 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330720507/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330720507 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/51 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/51' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n(C)n1) `ZINC001330720507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001330720507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330720507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001330720507 none COCCc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 9, 9, 9, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 9, 9, 9, 23, 23, 23, 22, 22, 22, 22, 9, 5, 1, 4, 4, 1, 1, 1, 1, 9, 9, 9] 50 rigid atoms, others: [34, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 40, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 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/323031/xbw-8058115.49/working/building/ZINC001330720507 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001330720507 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330720507/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330720507/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330720507 Building ZINC001330720507 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330720507' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330720507 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001330720507 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330720507/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330720507 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 50) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/50: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n(C)n1) `ZINC001330720507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001330720507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330720507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001330720507 none COCCc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 23, 23, 9, 9, 9, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 9, 9, 9, 24, 24, 24, 23, 23, 23, 23, 9, 5, 1, 4, 4, 1, 1, 1, 1, 9, 9, 9] 50 rigid atoms, others: [34, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 40, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 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/323031/xbw-8058115.49/working/building/ZINC001330720507 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330720507/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330720507 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 51) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/51: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n(C)n1) `ZINC001330720507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001330720507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330720507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001330720507 none COCCc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 9, 9, 9, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 9, 9, 9, 23, 23, 23, 22, 22, 22, 22, 9, 5, 1, 4, 4, 1, 1, 1, 1, 9, 9, 9] 50 rigid atoms, others: [34, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 40, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 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/323031/xbw-8058115.49/working/building/ZINC001330720507 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001330720507 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330720507/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330720507/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330720507 Building ZINC001330863564 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863564' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863564 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001330863564 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863564/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863564 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/52 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C[C@@H]1CCC(=O)N1)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001330863564.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001330863564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001330863564 none CC(C)N(C[C@@H]1CCC(=O)N1)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 7, 5, 5, 1, 11, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 4, 13, 15, 15, 15, 15, 15, 15, 1, 2, 1, 1, 1, 3, 3, 3, 10, 10, 10, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 12, 12, 15, 15, 15, 15, 15, 3, 10, 10, 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863564 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863564/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863564 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/53 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/53' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C[C@@H]1CCC(=O)N1)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001330863564.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001330863564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863564/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001330863564 none CC(C)N(C[C@@H]1CCC(=O)N1)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 7, 5, 5, 1, 11, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 5, 15, 20, 20, 20, 20, 20, 20, 1, 2, 1, 1, 1, 2, 2, 2, 6, 6, 6, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 13, 13, 20, 20, 20, 20, 20, 2, 6, 6, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 91 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863564 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001330863564 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863564/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863564/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863564 Building ZINC001330863564 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863564' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863564 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001330863564 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863564/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863564 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 52) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/52: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C[C@@H]1CCC(=O)N1)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001330863564.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001330863564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001330863564 none CC(C)N(C[C@@H]1CCC(=O)N1)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 7, 5, 5, 1, 11, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 4, 13, 15, 15, 15, 15, 15, 15, 1, 2, 1, 1, 1, 3, 3, 3, 10, 10, 10, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 12, 12, 15, 15, 15, 15, 15, 3, 10, 10, 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863564 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863564/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863564 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 53) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/53: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C[C@@H]1CCC(=O)N1)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001330863564.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001330863564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863564/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001330863564 none CC(C)N(C[C@@H]1CCC(=O)N1)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 7, 5, 5, 1, 11, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 5, 15, 20, 20, 20, 20, 20, 20, 1, 2, 1, 1, 1, 2, 2, 2, 6, 6, 6, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 13, 13, 20, 20, 20, 20, 20, 2, 6, 6, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 91 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863564 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001330863564 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863564/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863564/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863564 Building ZINC001330863565 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863565' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863565 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001330863565 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863565/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863565 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/54 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C[C@H]1CCC(=O)N1)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001330863565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001330863565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001330863565 none CC(C)N(C[C@H]1CCC(=O)N1)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 7, 5, 5, 1, 11, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 6, 2, 5, 14, 19, 19, 19, 19, 19, 19, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 12, 12, 19, 19, 19, 19, 19, 2, 7, 7, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863565 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863565/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863565 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/55 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/55' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C[C@H]1CCC(=O)N1)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001330863565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001330863565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001330863565 none CC(C)N(C[C@H]1CCC(=O)N1)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 7, 5, 5, 1, 11, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 5, 2, 4, 13, 14, 14, 14, 14, 14, 14, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 12, 12, 14, 14, 14, 14, 14, 2, 7, 7, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 80 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863565 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001330863565 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863565/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863565/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863565 Building ZINC001330863565 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863565' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863565 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001330863565 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863565/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863565 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 54) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/54: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C[C@H]1CCC(=O)N1)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001330863565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001330863565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001330863565 none CC(C)N(C[C@H]1CCC(=O)N1)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 7, 5, 5, 1, 11, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 6, 2, 5, 14, 19, 19, 19, 19, 19, 19, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 12, 12, 19, 19, 19, 19, 19, 2, 7, 7, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863565 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863565/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863565 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 55) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/55: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C[C@H]1CCC(=O)N1)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001330863565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001330863565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001330863565 none CC(C)N(C[C@H]1CCC(=O)N1)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 7, 5, 5, 1, 11, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 5, 2, 4, 13, 14, 14, 14, 14, 14, 14, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 12, 12, 14, 14, 14, 14, 14, 2, 7, 7, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 80 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863565 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001330863565 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863565/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863565/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330863565 Building ZINC001330956837 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956837' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956837 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001330956837 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956837/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956837 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/56 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@](C)(CCF)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001330956837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001330956837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001330956837 none COC(=O)[C@@](C)(CCF)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 15, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 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: [17, 17, 8, 17, 4, 8, 8, 14, 17, 4, 1, 4, 1, 1, 1, 3, 3, 3, 12, 12, 12, 3, 3, 3, 17, 17, 17, 8, 8, 8, 14, 14, 17, 17, 4, 3, 12, 12, 3, 3, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956837 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956837/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956837 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/57 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/57' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@](C)(CCF)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001330956837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001330956837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001330956837 none COC(=O)[C@@](C)(CCF)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 15, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 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: [12, 12, 7, 12, 3, 7, 7, 11, 13, 3, 1, 3, 1, 1, 1, 4, 4, 4, 15, 15, 15, 4, 4, 4, 12, 12, 12, 7, 7, 7, 11, 11, 13, 13, 3, 4, 15, 15, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956837 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001330956837 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956837/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956837/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956837 Building ZINC001330956837 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956837' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956837 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001330956837 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956837/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956837 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 56) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/56: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@](C)(CCF)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001330956837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001330956837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001330956837 none COC(=O)[C@@](C)(CCF)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 15, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 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: [17, 17, 8, 17, 4, 8, 8, 14, 17, 4, 1, 4, 1, 1, 1, 3, 3, 3, 12, 12, 12, 3, 3, 3, 17, 17, 17, 8, 8, 8, 14, 14, 17, 17, 4, 3, 12, 12, 3, 3, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956837 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956837/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956837 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 57) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/57: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@](C)(CCF)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001330956837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001330956837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001330956837 none COC(=O)[C@@](C)(CCF)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 15, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 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: [12, 12, 7, 12, 3, 7, 7, 11, 13, 3, 1, 3, 1, 1, 1, 4, 4, 4, 15, 15, 15, 4, 4, 4, 12, 12, 12, 7, 7, 7, 11, 11, 13, 13, 3, 4, 15, 15, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956837 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001330956837 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956837/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956837/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956837 Building ZINC001330956838 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956838' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956838 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001330956838 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956838/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956838 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/58 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@](C)(CCF)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001330956838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001330956838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001330956838 none COC(=O)[C@](C)(CCF)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 15, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 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: [12, 12, 7, 12, 3, 7, 7, 12, 14, 3, 1, 3, 1, 1, 1, 4, 4, 4, 14, 14, 14, 4, 4, 4, 12, 12, 12, 7, 7, 7, 12, 12, 14, 14, 3, 4, 14, 14, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956838 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956838/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956838 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/59 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/59' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@](C)(CCF)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001330956838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001330956838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001330956838 none COC(=O)[C@](C)(CCF)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 15, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 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: [17, 17, 8, 17, 4, 8, 8, 14, 17, 4, 1, 4, 1, 1, 1, 3, 3, 3, 12, 12, 12, 3, 3, 3, 17, 17, 17, 8, 8, 8, 14, 14, 17, 17, 4, 3, 12, 12, 3, 3, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956838 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001330956838 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956838/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956838/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956838 Building ZINC001330956838 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956838' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956838 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001330956838 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956838/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956838 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 58) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/58: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@](C)(CCF)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001330956838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001330956838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001330956838 none COC(=O)[C@](C)(CCF)NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 15, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 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: [12, 12, 7, 12, 3, 7, 7, 12, 14, 3, 1, 3, 1, 1, 1, 4, 4, 4, 14, 14, 14, 4, 4, 4, 12, 12, 12, 7, 7, 7, 12, 12, 14, 14, 3, 4, 14, 14, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956838 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956838/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956838 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 59) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/59: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@](C)(CCF)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001330956838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001330956838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001330956838 none COC(=O)[C@](C)(CCF)NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 15, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 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: [17, 17, 8, 17, 4, 8, 8, 14, 17, 4, 1, 4, 1, 1, 1, 3, 3, 3, 12, 12, 12, 3, 3, 3, 17, 17, 17, 8, 8, 8, 14, 14, 17, 17, 4, 3, 12, 12, 3, 3, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956838 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001330956838 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956838/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956838/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001330956838 Building ZINC001331171301 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171301' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171301 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001331171301 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171301/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171301 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/60 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](C(=O)C2CC2)C1) `ZINC001331171301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001331171301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001331171301 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](C(=O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 14, 14, 19, 19, 5, 1, 1, 1, 1, 4, 4, 1, 5, 5, 5, 5, 19, 19, 19, 19, 19, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171301 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171301/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171301 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/61 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/61' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](C(=O)C2CC2)C1) `ZINC001331171301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001331171301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001331171301 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](C(=O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 1, 1, 1, 1, 1, 2, 4, 5, 5, 5, 5, 5, 5, 17, 17, 21, 21, 5, 1, 1, 1, 1, 4, 4, 1, 5, 5, 5, 5, 21, 21, 21, 21, 21, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 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/323031/xbw-8058115.49/working/building/ZINC001331171301 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001331171301 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171301/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171301/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171301 Building ZINC001331171301 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171301' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171301 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001331171301 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171301/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171301 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 60) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/60: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](C(=O)C2CC2)C1) `ZINC001331171301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001331171301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001331171301 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](C(=O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 14, 14, 19, 19, 5, 1, 1, 1, 1, 4, 4, 1, 5, 5, 5, 5, 19, 19, 19, 19, 19, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171301 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171301/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171301 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 61) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/61: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](C(=O)C2CC2)C1) `ZINC001331171301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001331171301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001331171301 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](C(=O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 1, 1, 1, 1, 1, 2, 4, 5, 5, 5, 5, 5, 5, 17, 17, 21, 21, 5, 1, 1, 1, 1, 4, 4, 1, 5, 5, 5, 5, 21, 21, 21, 21, 21, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 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/323031/xbw-8058115.49/working/building/ZINC001331171301 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001331171301 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171301/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171301/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171301 Building ZINC001331171303 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171303' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171303 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001331171303 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171303/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171303 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/62 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](C(=O)C2CC2)C1) `ZINC001331171303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001331171303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001331171303 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](C(=O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 1, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 16, 16, 23, 23, 4, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 23, 23, 23, 23, 23, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 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/323031/xbw-8058115.49/working/building/ZINC001331171303 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171303/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171303 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/63 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/63' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](C(=O)C2CC2)C1) `ZINC001331171303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001331171303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001331171303 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](C(=O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 13, 13, 23, 23, 3, 1, 1, 1, 1, 4, 4, 1, 3, 3, 3, 3, 23, 23, 23, 23, 23, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 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/323031/xbw-8058115.49/working/building/ZINC001331171303 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001331171303 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171303/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171303/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171303 Building ZINC001331171303 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171303' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171303 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001331171303 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171303/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171303 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 62) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/62: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](C(=O)C2CC2)C1) `ZINC001331171303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001331171303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001331171303 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](C(=O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 1, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 16, 16, 23, 23, 4, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 23, 23, 23, 23, 23, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 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/323031/xbw-8058115.49/working/building/ZINC001331171303 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171303/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171303 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 63) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/63: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](C(=O)C2CC2)C1) `ZINC001331171303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001331171303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001331171303 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](C(=O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 13, 13, 23, 23, 3, 1, 1, 1, 1, 4, 4, 1, 3, 3, 3, 3, 23, 23, 23, 23, 23, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 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/323031/xbw-8058115.49/working/building/ZINC001331171303 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001331171303 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171303/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171303/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331171303 Building ZINC001331216209 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216209' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216209 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001331216209 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216209/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216209 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/64 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](O)CC12CCC2) `ZINC001331216209.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001331216209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001331216209 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](O)CC12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 14, 4, 1, 1, 1, 4, 9, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 4, 14, 14, 4, 11, 11, 11, 11, 33, 11, 11, 11, 11, 11, 11, 11, 11] 150 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 101 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216209 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216209/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216209 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/65 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/65' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](O)CC12CCC2) `ZINC001331216209.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001331216209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001331216209 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](O)CC12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 14, 4, 1, 1, 1, 4, 10, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4, 14, 14, 4, 13, 13, 13, 13, 39, 13, 13, 13, 13, 13, 13, 13, 13] 150 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 112 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216209 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001331216209 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216209/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216209/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216209 Building ZINC001331216209 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216209' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216209 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001331216209 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216209/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216209 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 64) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/64: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](O)CC12CCC2) `ZINC001331216209.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001331216209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001331216209 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](O)CC12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 14, 4, 1, 1, 1, 4, 9, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 4, 14, 14, 4, 11, 11, 11, 11, 33, 11, 11, 11, 11, 11, 11, 11, 11] 150 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 101 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216209 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216209/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216209 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 65) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/65: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](O)CC12CCC2) `ZINC001331216209.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001331216209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001331216209 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](O)CC12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 14, 4, 1, 1, 1, 4, 10, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4, 14, 14, 4, 13, 13, 13, 13, 39, 13, 13, 13, 13, 13, 13, 13, 13] 150 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 112 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216209 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001331216209 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216209/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216209/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216209 Building ZINC001331216212 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216212' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216212 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001331216212 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216212/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216212 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/66 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](O)CC12CCC2) `ZINC001331216212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001331216212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001331216212 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](O)CC12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 15, 4, 1, 1, 1, 3, 10, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4, 15, 15, 4, 13, 13, 13, 13, 39, 13, 13, 13, 13, 13, 13, 13, 13] 150 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216212 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216212/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216212 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/67 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/67' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](O)CC12CCC2) `ZINC001331216212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001331216212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001331216212 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](O)CC12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 12, 4, 1, 1, 1, 4, 10, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 12, 12, 4, 12, 12, 12, 12, 36, 12, 12, 12, 12, 12, 12, 12, 12] 150 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216212 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001331216212 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216212/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216212/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216212 Building ZINC001331216212 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216212' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216212 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001331216212 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216212/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216212 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 66) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/66: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](O)CC12CCC2) `ZINC001331216212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001331216212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001331216212 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](O)CC12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 15, 4, 1, 1, 1, 3, 10, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4, 15, 15, 4, 13, 13, 13, 13, 39, 13, 13, 13, 13, 13, 13, 13, 13] 150 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216212 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216212/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216212 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 67) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/67: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](O)CC12CCC2) `ZINC001331216212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001331216212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001331216212 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](O)CC12CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 12, 4, 1, 1, 1, 4, 10, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 12, 12, 4, 12, 12, 12, 12, 36, 12, 12, 12, 12, 12, 12, 12, 12] 150 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216212 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001331216212 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216212/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216212/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331216212 Building ZINC001331879064 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879064' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879064 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001331879064 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879064/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879064 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/68 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)CC2)CCOC1) `ZINC001331879064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001331879064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001331879064 none COC(=O)[C@]1(N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)CC2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 18, 31, 11, 11, 11, 11, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 11, 11, 18, 18, 18, 18, 31, 31, 31, 11, 11, 11, 11, 8, 8, 8, 8, 8, 11, 11, 11, 11, 18, 18, 18, 18, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 95 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879064 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879064/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879064 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/69 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/69' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)CC2)CCOC1) `ZINC001331879064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001331879064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001331879064 none COC(=O)[C@]1(N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)CC2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 17, 31, 11, 11, 11, 11, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 11, 11, 17, 17, 17, 17, 31, 31, 31, 11, 11, 11, 11, 4, 4, 4, 4, 4, 11, 11, 11, 11, 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]) total number of confs: 92 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879064 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001331879064 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879064/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879064/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879064 Building ZINC001331879064 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879064' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879064 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001331879064 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879064/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879064 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 68) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/68: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)CC2)CCOC1) `ZINC001331879064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001331879064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001331879064 none COC(=O)[C@]1(N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)CC2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 18, 31, 11, 11, 11, 11, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 11, 11, 18, 18, 18, 18, 31, 31, 31, 11, 11, 11, 11, 8, 8, 8, 8, 8, 11, 11, 11, 11, 18, 18, 18, 18, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 95 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879064 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879064/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879064 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 69) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/69: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)CC2)CCOC1) `ZINC001331879064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001331879064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001331879064 none COC(=O)[C@]1(N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)CC2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 17, 31, 11, 11, 11, 11, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 11, 11, 17, 17, 17, 17, 31, 31, 31, 11, 11, 11, 11, 4, 4, 4, 4, 4, 11, 11, 11, 11, 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]) total number of confs: 92 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879064 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001331879064 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879064/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879064/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879064 Building ZINC001331879065 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879065' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879065 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001331879065 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879065/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879065 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/70 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@]1(N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)CC2)CCOC1) `ZINC001331879065.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001331879065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001331879065 none COC(=O)[C@@]1(N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)CC2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 17, 31, 9, 9, 9, 9, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 17, 17, 17, 17, 31, 31, 31, 9, 9, 9, 9, 6, 6, 6, 6, 6, 9, 9, 9, 9, 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]) total number of confs: 103 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879065 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879065/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879065 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/71 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/71' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@]1(N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)CC2)CCOC1) `ZINC001331879065.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001331879065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879065/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001331879065 none COC(=O)[C@@]1(N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)CC2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 17, 30, 10, 10, 10, 10, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 17, 17, 17, 17, 30, 30, 30, 10, 10, 10, 10, 4, 4, 4, 4, 4, 10, 10, 10, 10, 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]) total number of confs: 95 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879065 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001331879065 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879065/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879065/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879065 Building ZINC001331879065 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879065' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879065 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001331879065 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879065/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879065 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 70) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/70: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@]1(N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)CC2)CCOC1) `ZINC001331879065.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001331879065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001331879065 none COC(=O)[C@@]1(N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)CC2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 17, 31, 9, 9, 9, 9, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 17, 17, 17, 17, 31, 31, 31, 9, 9, 9, 9, 6, 6, 6, 6, 6, 9, 9, 9, 9, 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]) total number of confs: 103 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879065 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879065/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879065 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 71) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/71: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@]1(N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)CC2)CCOC1) `ZINC001331879065.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001331879065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879065/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001331879065 none COC(=O)[C@@]1(N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)CC2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 17, 30, 10, 10, 10, 10, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 17, 17, 17, 17, 30, 30, 30, 10, 10, 10, 10, 4, 4, 4, 4, 4, 10, 10, 10, 10, 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]) total number of confs: 95 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879065 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001331879065 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879065/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879065/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001331879065 Building ZINC001332225474 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225474' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225474 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001332225474 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225474/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225474 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/72 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCS3(=O)=O)CC2)cn1) `ZINC001332225474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001332225474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001332225474 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCS3(=O)=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 7, 14, 14, 14, 14, 27, 32, 32, 32, 32, 32, 32, 32, 14, 14, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 19, 19, 32, 32, 32, 32, 32, 32, 14, 14, 14, 14, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 86 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225474 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225474/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225474 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/73 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/73' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCS3(=O)=O)CC2)cn1) `ZINC001332225474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001332225474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001332225474 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCS3(=O)=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 4, 7, 17, 17, 17, 17, 30, 33, 33, 33, 33, 33, 33, 33, 17, 17, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 22, 22, 33, 33, 33, 33, 33, 33, 17, 17, 17, 17, 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, 44, 45]) total number of confs: 82 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225474 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001332225474 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225474/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225474/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225474 Building ZINC001332225474 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225474' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225474 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001332225474 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225474/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225474 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 72) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/72: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCS3(=O)=O)CC2)cn1) `ZINC001332225474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001332225474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001332225474 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCS3(=O)=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 7, 14, 14, 14, 14, 27, 32, 32, 32, 32, 32, 32, 32, 14, 14, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 19, 19, 32, 32, 32, 32, 32, 32, 14, 14, 14, 14, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 86 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225474 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225474/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225474 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 73) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/73: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCS3(=O)=O)CC2)cn1) `ZINC001332225474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001332225474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001332225474 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCS3(=O)=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 4, 7, 17, 17, 17, 17, 30, 33, 33, 33, 33, 33, 33, 33, 17, 17, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 22, 22, 33, 33, 33, 33, 33, 33, 17, 17, 17, 17, 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, 44, 45]) total number of confs: 82 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225474 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001332225474 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225474/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225474/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225474 Building ZINC001332225475 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225475' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225475 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001332225475 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225475/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225475 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/74 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCS3(=O)=O)CC2)cn1) `ZINC001332225475.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001332225475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001332225475 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCS3(=O)=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 7, 14, 14, 14, 14, 27, 30, 30, 30, 30, 30, 30, 30, 14, 14, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 19, 19, 30, 30, 30, 30, 30, 30, 14, 14, 14, 14, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 84 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225475 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225475/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225475 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/75 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/75' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCS3(=O)=O)CC2)cn1) `ZINC001332225475.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001332225475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225475/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001332225475 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCS3(=O)=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 4, 8, 16, 16, 16, 16, 26, 30, 30, 30, 30, 30, 30, 30, 16, 16, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 18, 18, 30, 30, 30, 30, 30, 30, 16, 16, 16, 16, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225475 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001332225475 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225475/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225475/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225475 Building ZINC001332225475 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225475' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225475 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001332225475 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225475/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225475 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 74) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/74: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCS3(=O)=O)CC2)cn1) `ZINC001332225475.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001332225475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001332225475 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCS3(=O)=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 7, 14, 14, 14, 14, 27, 30, 30, 30, 30, 30, 30, 30, 14, 14, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 19, 19, 30, 30, 30, 30, 30, 30, 14, 14, 14, 14, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 84 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225475 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225475/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225475 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 75) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/75: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCS3(=O)=O)CC2)cn1) `ZINC001332225475.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001332225475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225475/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001332225475 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCS3(=O)=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 4, 8, 16, 16, 16, 16, 26, 30, 30, 30, 30, 30, 30, 30, 16, 16, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 18, 18, 30, 30, 30, 30, 30, 30, 16, 16, 16, 16, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225475 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001332225475 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225475/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225475/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001332225475 Building ZINC001334386789 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386789' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386789 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001334386789 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386789/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386789 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/76 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](N2CCC2)[C@H](F)C1) `ZINC001334386789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001334386789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001334386789 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](N2CCC2)[C@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 7, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 13, 13, 5, 1, 1, 1, 2, 6, 8, 11, 11, 11, 11, 12, 13, 13, 13, 11, 11, 11, 11, 5, 5, 5, 5, 13, 13, 5, 11, 11, 11, 11, 13, 13, 13, 13, 13, 13, 11, 11] 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386789 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386789/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386789 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/77 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/77' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](N2CCC2)[C@H](F)C1) `ZINC001334386789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001334386789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001334386789 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](N2CCC2)[C@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 7, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 4, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 8, 8, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386789 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001334386789 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386789/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386789/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386789 Building ZINC001334386789 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386789' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386789 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001334386789 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386789/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386789 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 76) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/76: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](N2CCC2)[C@H](F)C1) `ZINC001334386789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001334386789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001334386789 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](N2CCC2)[C@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 7, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 13, 13, 5, 1, 1, 1, 2, 6, 8, 11, 11, 11, 11, 12, 13, 13, 13, 11, 11, 11, 11, 5, 5, 5, 5, 13, 13, 5, 11, 11, 11, 11, 13, 13, 13, 13, 13, 13, 11, 11] 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386789 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386789/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386789 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 77) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/77: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](N2CCC2)[C@H](F)C1) `ZINC001334386789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001334386789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001334386789 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](N2CCC2)[C@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 7, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 4, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 8, 8, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386789 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001334386789 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386789/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386789/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386789 Building ZINC001334386790 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386790' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386790 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001334386790 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386790/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386790 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/78 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCC2)[C@@H](F)C1) `ZINC001334386790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001334386790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001334386790 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCC2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 7, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 9, 3, 1, 1, 1, 1, 8, 8, 11, 11, 11, 11, 12, 14, 14, 14, 11, 11, 11, 11, 3, 3, 3, 3, 9, 9, 3, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 11, 11] 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, 42, 43, 44, 45]) total number of confs: 55 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386790 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386790/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386790 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/79 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/79' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCC2)[C@@H](F)C1) `ZINC001334386790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001334386790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001334386790 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCC2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 7, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 1, 8, 8, 11, 11, 11, 11, 11, 12, 12, 12, 11, 11, 11, 11, 2, 2, 2, 2, 8, 8, 2, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 11, 11] 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, 42, 43, 44, 45]) total number of confs: 51 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386790 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001334386790 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386790/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386790/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386790 Building ZINC001334386790 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386790' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386790 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001334386790 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386790/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386790 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 78) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/78: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCC2)[C@@H](F)C1) `ZINC001334386790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001334386790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001334386790 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCC2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 7, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 9, 3, 1, 1, 1, 1, 8, 8, 11, 11, 11, 11, 12, 14, 14, 14, 11, 11, 11, 11, 3, 3, 3, 3, 9, 9, 3, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 11, 11] 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, 42, 43, 44, 45]) total number of confs: 55 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386790 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386790/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386790 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 79) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/79: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCC2)[C@@H](F)C1) `ZINC001334386790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001334386790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001334386790 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCC2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 7, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 1, 8, 8, 11, 11, 11, 11, 11, 12, 12, 12, 11, 11, 11, 11, 2, 2, 2, 2, 8, 8, 2, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 11, 11] 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, 42, 43, 44, 45]) total number of confs: 51 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386790 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001334386790 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386790/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386790/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386790 Building ZINC001334386791 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386791' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386791 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001334386791 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386791/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386791 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/80 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](N2CCC2)[C@@H](F)C1) `ZINC001334386791.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001334386791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001334386791 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](N2CCC2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 7, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 9, 3, 1, 1, 1, 1, 7, 9, 12, 12, 12, 12, 12, 13, 13, 13, 12, 12, 12, 12, 3, 3, 3, 3, 9, 9, 3, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 12, 12] 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, 42, 43, 44, 45]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386791 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386791/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386791 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/81 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/81' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](N2CCC2)[C@@H](F)C1) `ZINC001334386791.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001334386791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001334386791 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](N2CCC2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 7, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 12, 12, 5, 1, 1, 1, 2, 7, 9, 12, 12, 12, 12, 13, 16, 16, 16, 12, 12, 12, 12, 5, 5, 5, 5, 12, 12, 5, 12, 12, 12, 12, 16, 16, 16, 16, 16, 16, 12, 12] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386791 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001334386791 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386791/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386791/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386791 Building ZINC001334386791 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386791' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386791 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001334386791 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386791/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386791 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 80) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/80: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](N2CCC2)[C@@H](F)C1) `ZINC001334386791.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001334386791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001334386791 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](N2CCC2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 7, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 9, 3, 1, 1, 1, 1, 7, 9, 12, 12, 12, 12, 12, 13, 13, 13, 12, 12, 12, 12, 3, 3, 3, 3, 9, 9, 3, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 12, 12] 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, 42, 43, 44, 45]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386791 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386791/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386791 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 81) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/81: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](N2CCC2)[C@@H](F)C1) `ZINC001334386791.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001334386791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001334386791 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](N2CCC2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 7, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 12, 12, 5, 1, 1, 1, 2, 7, 9, 12, 12, 12, 12, 13, 16, 16, 16, 12, 12, 12, 12, 5, 5, 5, 5, 12, 12, 5, 12, 12, 12, 12, 16, 16, 16, 16, 16, 16, 12, 12] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386791 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001334386791 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386791/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386791/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386791 Building ZINC001334386792 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386792' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386792 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001334386792 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386792/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386792 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/82 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCC2)[C@H](F)C1) `ZINC001334386792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001334386792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001334386792 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCC2)[C@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 7, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 1, 8, 11, 12, 12, 12, 12, 13, 15, 15, 15, 12, 12, 12, 12, 2, 2, 2, 2, 8, 8, 2, 12, 12, 12, 12, 15, 15, 15, 15, 15, 15, 12, 12] 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, 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/323031/xbw-8058115.49/working/building/ZINC001334386792 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386792/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386792 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/83 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/83' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCC2)[C@H](F)C1) `ZINC001334386792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001334386792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001334386792 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCC2)[C@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 7, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 2, 1, 1, 1, 1, 8, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 2, 7, 7, 2, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 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, 42, 43, 44, 45]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386792 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001334386792 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386792/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386792/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386792 Building ZINC001334386792 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386792' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386792 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001334386792 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386792/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386792 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 82) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/82: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCC2)[C@H](F)C1) `ZINC001334386792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001334386792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001334386792 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCC2)[C@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 7, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 1, 8, 11, 12, 12, 12, 12, 13, 15, 15, 15, 12, 12, 12, 12, 2, 2, 2, 2, 8, 8, 2, 12, 12, 12, 12, 15, 15, 15, 15, 15, 15, 12, 12] 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, 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/323031/xbw-8058115.49/working/building/ZINC001334386792 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386792/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386792 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 83) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/83: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCC2)[C@H](F)C1) `ZINC001334386792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001334386792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001334386792 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCC2)[C@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 7, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 2, 1, 1, 1, 1, 8, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 2, 7, 7, 2, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 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, 42, 43, 44, 45]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386792 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001334386792 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386792/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386792/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334386792 Building ZINC001334452451 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334452451' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334452451 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001334452451 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334452451/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334452451 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/84 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(C2(O)CC2)CC1) `ZINC001334452451.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001334452451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334452451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001334452451 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(C2(O)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 9, 3, 1, 1, 1, 1, 3, 5, 8, 8, 8, 8, 12, 12, 12, 8, 8, 3, 3, 3, 3, 9, 9, 3, 8, 8, 8, 8, 8, 36, 12, 12, 12, 12, 8, 8, 8, 8] 150 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, 42, 43, 44]) total number of confs: 90 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334452451 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334452451/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334452451 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/85 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/85' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(C2(O)CC2)CC1) `ZINC001334452451.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001334452451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334452451/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001334452451 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(C2(O)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 1, 2, 4, 7, 7, 7, 7, 12, 12, 12, 7, 7, 2, 2, 2, 2, 8, 8, 2, 7, 7, 7, 7, 7, 36, 12, 12, 12, 12, 7, 7, 7, 7] 150 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, 42, 43, 44]) total number of confs: 89 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334452451 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001334452451 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334452451/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334452451/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334452451 Building ZINC001334452451 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334452451' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334452451 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001334452451 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334452451/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334452451 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 84) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/84: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(C2(O)CC2)CC1) `ZINC001334452451.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001334452451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334452451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001334452451 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(C2(O)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 9, 3, 1, 1, 1, 1, 3, 5, 8, 8, 8, 8, 12, 12, 12, 8, 8, 3, 3, 3, 3, 9, 9, 3, 8, 8, 8, 8, 8, 36, 12, 12, 12, 12, 8, 8, 8, 8] 150 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, 42, 43, 44]) total number of confs: 90 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334452451 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334452451/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334452451 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 85) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/85: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(C2(O)CC2)CC1) `ZINC001334452451.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001334452451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334452451/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001334452451 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(C2(O)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 1, 2, 4, 7, 7, 7, 7, 12, 12, 12, 7, 7, 2, 2, 2, 2, 8, 8, 2, 7, 7, 7, 7, 7, 36, 12, 12, 12, 12, 7, 7, 7, 7] 150 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, 42, 43, 44]) total number of confs: 89 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334452451 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001334452451 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334452451/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334452451/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334452451 Building ZINC001334473539 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473539' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473539 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001334473539 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473539/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473539 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/86 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H]1CCOC1) `ZINC001334473539.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001334473539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001334473539 none CO[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 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] 0 hydrogens 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, 13, 20, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 20, 24, 24, 24, 24, 24, 20, 20, 20, 13, 13, 3, 2, 5, 5, 2, 2, 2, 2, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473539 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473539/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473539 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/87 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/87' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H]1CCOC1) `ZINC001334473539.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001334473539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473539/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001334473539 none CO[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 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] 0 hydrogens 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, 15, 19, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 19, 25, 25, 25, 25, 25, 19, 19, 19, 15, 15, 3, 3, 6, 6, 3, 3, 3, 3, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473539 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001334473539 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473539/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473539/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473539 Building ZINC001334473539 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473539' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473539 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001334473539 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473539/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473539 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 86) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/86: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H]1CCOC1) `ZINC001334473539.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001334473539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001334473539 none CO[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 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] 0 hydrogens 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, 13, 20, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 20, 24, 24, 24, 24, 24, 20, 20, 20, 13, 13, 3, 2, 5, 5, 2, 2, 2, 2, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473539 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473539/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473539 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 87) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/87: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H]1CCOC1) `ZINC001334473539.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001334473539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473539/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001334473539 none CO[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 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] 0 hydrogens 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, 15, 19, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 19, 25, 25, 25, 25, 25, 19, 19, 19, 15, 15, 3, 3, 6, 6, 3, 3, 3, 3, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473539 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001334473539 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473539/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473539/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473539 Building ZINC001334473540 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473540' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473540 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001334473540 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473540/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473540 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/88 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CCOC1) `ZINC001334473540.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001334473540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001334473540 none CO[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 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] 0 hydrogens 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, 15, 19, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 19, 24, 24, 24, 24, 24, 19, 19, 19, 15, 15, 3, 3, 6, 6, 3, 3, 3, 3, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473540 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473540/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473540 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/89 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/89' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CCOC1) `ZINC001334473540.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001334473540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473540/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001334473540 none CO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 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] 0 hydrogens 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, 13, 21, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 21, 25, 25, 25, 25, 25, 21, 21, 21, 13, 13, 3, 2, 5, 5, 2, 2, 2, 2, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473540 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001334473540 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473540/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473540/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473540 Building ZINC001334473540 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473540' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473540 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001334473540 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473540/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473540 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 88) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/88: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CCOC1) `ZINC001334473540.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001334473540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001334473540 none CO[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 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] 0 hydrogens 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, 15, 19, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 19, 24, 24, 24, 24, 24, 19, 19, 19, 15, 15, 3, 3, 6, 6, 3, 3, 3, 3, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473540 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473540/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473540 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 89) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/89: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CCOC1) `ZINC001334473540.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001334473540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473540/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001334473540 none CO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 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] 0 hydrogens 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, 13, 21, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 21, 25, 25, 25, 25, 25, 21, 21, 21, 13, 13, 3, 2, 5, 5, 2, 2, 2, 2, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473540 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001334473540 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473540/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473540/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473540 Building ZINC001334473541 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473541' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473541 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001334473541 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473541/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473541 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/90 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CCOC1) `ZINC001334473541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001334473541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001334473541 none CO[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 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] 0 hydrogens 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, 13, 21, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 21, 26, 26, 26, 26, 26, 21, 21, 21, 13, 13, 2, 2, 5, 5, 2, 2, 2, 2, 26, 26, 26, 26, 26, 26] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473541 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473541/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473541 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/91 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/91' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CCOC1) `ZINC001334473541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001334473541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001334473541 none CO[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 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] 0 hydrogens 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, 14, 18, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 18, 25, 25, 25, 25, 25, 18, 18, 18, 14, 14, 2, 2, 5, 5, 2, 2, 2, 2, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473541 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001334473541 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473541/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473541/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473541 Building ZINC001334473541 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473541' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473541 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001334473541 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473541/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473541 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 90) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/90: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CCOC1) `ZINC001334473541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001334473541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001334473541 none CO[C@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 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] 0 hydrogens 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, 13, 21, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 21, 26, 26, 26, 26, 26, 21, 21, 21, 13, 13, 2, 2, 5, 5, 2, 2, 2, 2, 26, 26, 26, 26, 26, 26] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473541 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473541/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473541 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 91) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/91: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CCOC1) `ZINC001334473541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001334473541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001334473541 none CO[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 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] 0 hydrogens 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, 14, 18, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 18, 25, 25, 25, 25, 25, 18, 18, 18, 14, 14, 2, 2, 5, 5, 2, 2, 2, 2, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473541 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001334473541 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473541/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473541/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473541 Building ZINC001334473542 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473542' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473542 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001334473542 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473542/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473542 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/92 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H]1CCOC1) `ZINC001334473542.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001334473542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001334473542 none CO[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 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] 0 hydrogens 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, 14, 18, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 18, 25, 25, 25, 25, 25, 18, 18, 18, 14, 14, 2, 2, 5, 5, 2, 2, 2, 2, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473542 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473542/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473542 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/93 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/93' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H]1CCOC1) `ZINC001334473542.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001334473542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473542/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001334473542 none CO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 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] 0 hydrogens 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, 14, 21, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 21, 26, 26, 26, 26, 26, 21, 21, 21, 14, 14, 3, 2, 5, 5, 2, 2, 2, 2, 26, 26, 26, 26, 26, 26] 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473542 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001334473542 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473542/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473542/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473542 Building ZINC001334473542 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473542' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473542 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001334473542 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473542/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473542 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 92) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/92: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H]1CCOC1) `ZINC001334473542.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001334473542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001334473542 none CO[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 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] 0 hydrogens 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, 14, 18, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 18, 25, 25, 25, 25, 25, 18, 18, 18, 14, 14, 2, 2, 5, 5, 2, 2, 2, 2, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473542 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473542/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473542 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 93) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/93: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H]1CCOC1) `ZINC001334473542.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001334473542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473542/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001334473542 none CO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 6, 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, 4, 6, 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] 0 hydrogens 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, 14, 21, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 21, 26, 26, 26, 26, 26, 21, 21, 21, 14, 14, 3, 2, 5, 5, 2, 2, 2, 2, 26, 26, 26, 26, 26, 26] 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473542 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001334473542 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473542/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473542/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334473542 Building ZINC001334968890 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968890' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968890 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001334968890 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968890/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968890 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/94 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001334968890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001334968890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001334968890 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 21, 21, 21, 26, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 50, 50, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968890 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968890/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968890 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/95 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/95' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001334968890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001334968890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001334968890 none C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 17, 17, 17, 24, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 50, 50, 50, 50, 50, 50, 17, 17] 50 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968890 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001334968890 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968890/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968890/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968890 Building ZINC001334968890 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968890' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968890 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001334968890 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968890/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968890 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 94) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/94: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001334968890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001334968890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001334968890 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 21, 21, 21, 26, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 50, 50, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968890 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968890/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968890 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 95) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/95: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001334968890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001334968890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001334968890 none C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 17, 17, 17, 24, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 50, 50, 50, 50, 50, 50, 17, 17] 50 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968890 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001334968890 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968890/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968890/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968890 Building ZINC001334968896 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968896' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968896 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001334968896 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968896/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968896 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/96 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001334968896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001334968896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001334968896 none C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 18, 18, 18, 23, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 50, 50, 50, 50, 50, 50, 18, 18] 50 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968896 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968896/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968896 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/97 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/97' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001334968896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001334968896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001334968896 none C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 22, 22, 22, 27, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 50, 50, 50, 50, 50, 50, 22, 22] 50 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968896 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001334968896 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968896/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968896/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968896 Building ZINC001334968896 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968896' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968896 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001334968896 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968896/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968896 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 96) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/96: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001334968896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001334968896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001334968896 none C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 18, 18, 18, 23, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 50, 50, 50, 50, 50, 50, 18, 18] 50 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968896 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968896/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968896 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 97) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/97: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001334968896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001334968896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001334968896 none C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 22, 22, 22, 27, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 50, 50, 50, 50, 50, 50, 22, 22] 50 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 36, 38, 39] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968896 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001334968896 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968896/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968896/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001334968896 Building ZINC001335401434 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401434' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401434 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001335401434 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401434/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401434 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/98 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCC2)C1=O) `ZINC001335401434.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001335401434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001335401434 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 6, 9, 9, 9, 9, 9, 21, 21, 21, 9, 9, 1, 1, 1, 1, 4, 4, 1, 3, 9, 9, 9, 9, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 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/323031/xbw-8058115.49/working/building/ZINC001335401434 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401434/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401434 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/99 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/99' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCC2)C1=O) `ZINC001335401434.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001335401434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401434/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001335401434 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 5, 5, 5, 5, 5, 15, 15, 15, 5, 5, 1, 1, 1, 1, 4, 4, 1, 2, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401434 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001335401434 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401434/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401434/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401434 Building ZINC001335401434 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401434' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401434 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001335401434 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401434/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401434 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 98) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/98: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCC2)C1=O) `ZINC001335401434.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001335401434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001335401434 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 6, 9, 9, 9, 9, 9, 21, 21, 21, 9, 9, 1, 1, 1, 1, 4, 4, 1, 3, 9, 9, 9, 9, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 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/323031/xbw-8058115.49/working/building/ZINC001335401434 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401434/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401434 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 99) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/99: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCC2)C1=O) `ZINC001335401434.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001335401434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401434/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001335401434 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C2CCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 5, 5, 5, 5, 5, 15, 15, 15, 5, 5, 1, 1, 1, 1, 4, 4, 1, 2, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401434 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001335401434 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401434/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401434/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401434 Building ZINC001335401435 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401435' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401435 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001335401435 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401435/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401435 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/100 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCC2)C1=O) `ZINC001335401435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001335401435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001335401435 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 7, 7, 7, 7, 7, 17, 17, 17, 7, 7, 1, 1, 1, 1, 4, 4, 1, 2, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 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/323031/xbw-8058115.49/working/building/ZINC001335401435 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401435/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401435 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/101 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/101' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCC2)C1=O) `ZINC001335401435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001335401435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001335401435 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 24, 24, 24, 11, 11, 1, 1, 1, 1, 4, 4, 1, 3, 11, 11, 11, 11, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401435 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001335401435 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401435/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401435/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401435 Building ZINC001335401435 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401435' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401435 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001335401435 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401435/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401435 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 100) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/100: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCC2)C1=O) `ZINC001335401435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001335401435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001335401435 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 4, 7, 7, 7, 7, 7, 17, 17, 17, 7, 7, 1, 1, 1, 1, 4, 4, 1, 2, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 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/323031/xbw-8058115.49/working/building/ZINC001335401435 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401435/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401435 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 101) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/101: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCC2)C1=O) `ZINC001335401435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001335401435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001335401435 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C2CCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 5, 11, 11, 11, 11, 11, 24, 24, 24, 11, 11, 1, 1, 1, 1, 4, 4, 1, 3, 11, 11, 11, 11, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401435 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001335401435 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401435/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401435/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001335401435 Building ZINC001337863230 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863230' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863230 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001337863230 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863230/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863230 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/102 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1[C@@H]1C[C@H]1C(=O)NC[C@H](CO)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001337863230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001337863230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001337863230 none Cn1cncc1[C@@H]1C[C@H]1C(=O)NC[C@H](CO)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 45, 45, 45, 45, 24, 45, 24, 24, 17, 7, 2, 7, 7, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 45, 45, 24, 17, 17, 13, 13, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 244 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863230 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863230/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863230 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/103 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/103' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1[C@@H]1C[C@H]1C(=O)NC[C@H](CO)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001337863230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001337863230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001337863230 none Cn1cncc1[C@@H]1C[C@H]1C(=O)NC[C@H](CO)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 45, 45, 45, 45, 26, 45, 26, 26, 18, 9, 2, 9, 9, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 45, 45, 26, 18, 18, 14, 14, 42, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 247 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863230 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001337863230 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863230/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863230/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863230 Building ZINC001337863230 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863230' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863230 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001337863230 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863230/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863230 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 102) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/102: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1[C@@H]1C[C@H]1C(=O)NC[C@H](CO)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001337863230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001337863230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001337863230 none Cn1cncc1[C@@H]1C[C@H]1C(=O)NC[C@H](CO)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 45, 45, 45, 45, 24, 45, 24, 24, 17, 7, 2, 7, 7, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 45, 45, 24, 17, 17, 13, 13, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 244 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863230 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863230/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863230 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 103) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/103: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1[C@@H]1C[C@H]1C(=O)NC[C@H](CO)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001337863230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001337863230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001337863230 none Cn1cncc1[C@@H]1C[C@H]1C(=O)NC[C@H](CO)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 45, 45, 45, 45, 26, 45, 26, 26, 18, 9, 2, 9, 9, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 45, 45, 26, 18, 18, 14, 14, 42, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 247 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863230 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001337863230 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863230/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863230/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863230 Building ZINC001337863231 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863231' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863231 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001337863231 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863231/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863231 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/104 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1[C@@H]1C[C@H]1C(=O)NC[C@@H](CO)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001337863231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001337863231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001337863231 none Cn1cncc1[C@@H]1C[C@H]1C(=O)NC[C@@H](CO)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 47, 47, 47, 28, 47, 28, 28, 18, 9, 2, 9, 9, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 47, 47, 28, 18, 18, 13, 13, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 243 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863231 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863231/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863231 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/105 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/105' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1[C@@H]1C[C@H]1C(=O)NC[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001337863231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001337863231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001337863231 none Cn1cncc1[C@@H]1C[C@H]1C(=O)NC[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 49, 49, 49, 49, 28, 49, 28, 28, 18, 7, 2, 7, 7, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 49, 49, 28, 18, 18, 13, 13, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 258 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863231 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001337863231 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863231/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863231/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863231 Building ZINC001337863231 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863231' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863231 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001337863231 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863231/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863231 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 104) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/104: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1[C@@H]1C[C@H]1C(=O)NC[C@@H](CO)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001337863231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001337863231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001337863231 none Cn1cncc1[C@@H]1C[C@H]1C(=O)NC[C@@H](CO)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 47, 47, 47, 47, 28, 47, 28, 28, 18, 9, 2, 9, 9, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 47, 47, 28, 18, 18, 13, 13, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 243 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863231 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863231/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863231 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 105) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/105: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1[C@@H]1C[C@H]1C(=O)NC[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001337863231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001337863231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001337863231 none Cn1cncc1[C@@H]1C[C@H]1C(=O)NC[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 49, 49, 49, 49, 28, 49, 28, 28, 18, 7, 2, 7, 7, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 49, 49, 28, 18, 18, 13, 13, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 258 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863231 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001337863231 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863231/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863231/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001337863231 Building ZINC001339163068 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163068 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/106 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001339163068.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163068 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 20, 20, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 20, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 40, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/107 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/107' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001339163068.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163068 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 20, 20, 28, 49, 49, 49, 49, 49, 49, 50, 50, 49, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 49, 49, 49, 49, 50, 50, 6, 6] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 40, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/108 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/108' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001339163068.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163068 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 19, 19, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 19, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 40, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/109 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/109' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001339163068.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163068 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 20, 20, 28, 49, 49, 49, 49, 49, 49, 50, 50, 49, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 49, 49, 49, 49, 50, 50, 6, 6] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 40, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001339163068 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 Building ZINC001339163068 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163068 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 106) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/106: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001339163068.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163068 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 20, 20, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 20, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 40, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 107) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/107: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001339163068.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163068 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 20, 20, 28, 49, 49, 49, 49, 49, 49, 50, 50, 49, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 49, 49, 49, 49, 50, 50, 6, 6] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 40, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 108) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/108: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001339163068.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163068 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 19, 19, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 19, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 40, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 109) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/109: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001339163068.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163068 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 20, 20, 28, 49, 49, 49, 49, 49, 49, 50, 50, 49, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 49, 49, 49, 49, 50, 50, 6, 6] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 40, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001339163068 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 Building ZINC001339163068 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163068 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 106) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/106: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001339163068.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163068 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 20, 20, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 20, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 40, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 107) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/107: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001339163068.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163068 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 20, 20, 28, 49, 49, 49, 49, 49, 49, 50, 50, 49, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 49, 49, 49, 49, 50, 50, 6, 6] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 40, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 108) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/108: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001339163068.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163068 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 19, 19, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 19, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 40, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 109) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/109: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001339163068.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163068 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 20, 20, 28, 49, 49, 49, 49, 49, 49, 50, 50, 49, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 49, 49, 49, 49, 50, 50, 6, 6] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 40, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001339163068 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 Building ZINC001339163068 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001339163068 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 106) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/106: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001339163068.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001339163068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163068 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 20, 20, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 20, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 40, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 107) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/107: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001339163068.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001339163068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163068 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 20, 20, 28, 49, 49, 49, 49, 49, 49, 50, 50, 49, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 49, 49, 49, 49, 50, 50, 6, 6] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 40, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 108) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/108: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001339163068.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001339163068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163068 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 19, 19, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 19, 50, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 40, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 109) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/109: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001339163068.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001339163068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001339163068 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 20, 20, 28, 49, 49, 49, 49, 49, 49, 50, 50, 49, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 49, 49, 49, 49, 50, 50, 6, 6] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 40, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001339163068 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001339163068 Building ZINC001341050165 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341050165' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341050165 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341050165 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341050165/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341050165 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/110 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NCCC(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001341050165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341050165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341050165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001341050165 none COCC(=O)NCCC(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 28, 28, 28, 23, 19, 10, 8, 10, 8, 8, 8, 8, 8, 8, 3, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 50, 28, 23, 23, 19, 19, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341050165 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341050165/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341050165 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/111 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/111' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NCCC(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001341050165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341050165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341050165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001341050165 none COCC(=O)NCCC(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 20, 20, 20, 19, 15, 10, 7, 10, 7, 7, 7, 7, 7, 7, 3, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 20, 19, 19, 15, 15, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341050165 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341050165 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341050165/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341050165/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341050165 Building ZINC001341050165 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341050165' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341050165 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341050165 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341050165/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341050165 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 110) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/110: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NCCC(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001341050165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341050165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341050165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001341050165 none COCC(=O)NCCC(=O)N1CC[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 28, 28, 28, 23, 19, 10, 8, 10, 8, 8, 8, 8, 8, 8, 3, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 50, 28, 23, 23, 19, 19, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341050165 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341050165/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341050165 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 111) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/111: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NCCC(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001341050165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341050165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341050165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001341050165 none COCC(=O)NCCC(=O)N1CC[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 20, 20, 20, 19, 15, 10, 7, 10, 7, 7, 7, 7, 7, 7, 3, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 20, 19, 19, 15, 15, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341050165 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341050165 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341050165/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341050165/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341050165 Building ZINC001341314384 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314384' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314384 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314384 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314384/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314384 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/112 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1n[nH]c(C)c1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341314384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001341314384 none Cc1n[nH]c(C)c1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 6, 1, 5, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 48, 24, 11, 24, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 48, 48, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 216 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314384 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314384/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314384 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 113) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/113 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/113' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1n[nH]c(C)c1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341314384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001341314384 none Cc1n[nH]c(C)c1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 6, 1, 5, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 48, 23, 11, 23, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 48, 48, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 218 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314384 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341314384 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314384/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314384/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314384 Building ZINC001341314384 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314384' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314384 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314384 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314384/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314384 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 112) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/112: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1n[nH]c(C)c1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341314384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001341314384 none Cc1n[nH]c(C)c1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 6, 1, 5, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 48, 24, 11, 24, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 48, 48, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 216 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314384 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314384/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314384 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 113) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/113: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1n[nH]c(C)c1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341314384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001341314384 none Cc1n[nH]c(C)c1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 6, 1, 5, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 48, 23, 11, 23, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 48, 48, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 218 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314384 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341314384 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314384/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314384/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314384 Building ZINC001341314442 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314442' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314442 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314442 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314442/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314442 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/114 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(C(N)=O)cc2)C[C@H]1O) `ZINC001341314442.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001341314442 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(C(N)=O)cc2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 14, 14, 14, 14, 30, 30, 37, 37, 30, 35, 50, 50, 37, 37, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 37, 37, 50, 50, 37, 37, 14, 14, 42] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314442 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314442/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314442 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 115) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/115 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/115' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(C(N)=O)cc2)C[C@H]1O) `ZINC001341314442.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001341314442 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(C(N)=O)cc2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 27, 27, 34, 34, 27, 31, 50, 50, 34, 34, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 34, 34, 50, 50, 34, 34, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314442 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341314442 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314442/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314442/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314442 Building ZINC001341314442 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314442' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314442 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314442 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314442/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314442 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 114) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/114: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(C(N)=O)cc2)C[C@H]1O) `ZINC001341314442.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001341314442 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(C(N)=O)cc2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 14, 14, 14, 14, 30, 30, 37, 37, 30, 35, 50, 50, 37, 37, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 37, 37, 50, 50, 37, 37, 14, 14, 42] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314442 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314442/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314442 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 115) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/115: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(C(N)=O)cc2)C[C@H]1O) `ZINC001341314442.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001341314442 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(C(N)=O)cc2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 27, 27, 34, 34, 27, 31, 50, 50, 34, 34, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 34, 34, 50, 50, 34, 34, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314442 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341314442 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314442/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314442/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314442 Building ZINC001341314604 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314604' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314604 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314604/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/116 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001341314604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341314604 none C[C@@H]1CCN(C(=O)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 46, 18, 30, 9, 18, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314604/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 117) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/117 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/117' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001341314604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341314604 none C[C@@H]1CCN(C(=O)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 48, 19, 30, 9, 19, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341314604 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314604/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314604/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314604 Building ZINC001341314604 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314604' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314604 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314604/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 116) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/116: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001341314604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341314604 none C[C@@H]1CCN(C(=O)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 46, 18, 30, 9, 18, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314604/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 117) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/117: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001341314604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341314604 none C[C@@H]1CCN(C(=O)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 48, 19, 30, 9, 19, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341314604 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314604/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314604/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314604 Building ZINC001341314605 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314605' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314605 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314605 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314605/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314605 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/118 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001341314605.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341314605 none C[C@H]1CCN(C(=O)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 46, 18, 29, 9, 18, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314605 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314605/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314605 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 119) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/119 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/119' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001341314605.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314605/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341314605 none C[C@H]1CCN(C(=O)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 49, 19, 31, 8, 19, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314605 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341314605 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314605/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314605/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314605 Building ZINC001341314605 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314605' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314605 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314605 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314605/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314605 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 118) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/118: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001341314605.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341314605 none C[C@H]1CCN(C(=O)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 46, 18, 29, 9, 18, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314605 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314605/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314605 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 119) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/119: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001341314605.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314605/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341314605 none C[C@H]1CCN(C(=O)C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 49, 19, 31, 8, 19, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314605 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341314605 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314605/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314605/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314605 Building ZINC001341314624 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314624' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314624 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314624 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314624/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314624 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/120 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C(=O)CC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341314624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001341314624 none CC(C)N1C(=O)CC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 27, 50, 11, 27, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 186 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314624 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314624/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314624 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 121) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/121 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/121' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C(=O)CC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341314624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001341314624 none CC(C)N1C(=O)CC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 28, 50, 12, 28, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 193 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314624 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341314624 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314624/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314624/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314624 Building ZINC001341314624 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314624' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314624 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314624 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314624/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314624 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 120) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/120: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C(=O)CC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341314624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001341314624 none CC(C)N1C(=O)CC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 27, 50, 11, 27, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 186 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314624 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314624/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314624 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 121) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/121: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C(=O)CC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341314624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001341314624 none CC(C)N1C(=O)CC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 28, 50, 12, 28, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54]) total number of confs: 193 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314624 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341314624 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314624/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314624/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314624 Building ZINC001341314877 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314877' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314877 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314877 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314877/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314877 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/122 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3[nH]cnc3c2)C[C@H]1O) `ZINC001341314877.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001341314877 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3[nH]cnc3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 1, 8, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314877 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314877/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314877 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 123) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/123 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/123' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3[nH]cnc3c2)C[C@H]1O) `ZINC001341314877.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001341314877 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3[nH]cnc3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 1, 8, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314877 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341314877 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314877/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314877/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314877 Building ZINC001341314877 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314877' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314877 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341314877 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314877/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314877 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 122) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/122: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3[nH]cnc3c2)C[C@H]1O) `ZINC001341314877.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341314877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001341314877 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3[nH]cnc3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 1, 8, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314877 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314877/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314877 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 123) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/123: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3[nH]cnc3c2)C[C@H]1O) `ZINC001341314877.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341314877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001341314877 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3[nH]cnc3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 1, 8, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314877 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341314877 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314877/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314877/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341314877 Building ZINC001341315114 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315114' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315114 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315114 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315114/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315114 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/124 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N1CCOCC1) `ZINC001341315114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341315114 none C[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 26, 48, 11, 26, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 48, 50, 50, 50, 50, 50, 48, 48, 48, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 218 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315114 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315114/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315114 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 125) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/125 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/125' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N1CCOCC1) `ZINC001341315114.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341315114 none C[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 25, 50, 10, 25, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 222 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315114 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341315114 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315114/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315114/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315114 Building ZINC001341315114 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315114' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315114 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315114 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315114/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315114 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 124) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/124: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N1CCOCC1) `ZINC001341315114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341315114 none C[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 26, 48, 11, 26, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 48, 50, 50, 50, 50, 50, 48, 48, 48, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 218 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315114 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315114/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315114 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 125) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/125: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N1CCOCC1) `ZINC001341315114.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341315114 none C[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 25, 50, 10, 25, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 222 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315114 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341315114 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315114/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315114/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315114 Building ZINC001341315191 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315191' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315191 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315191 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315191/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315191 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/126 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCn2ccnn2)C[C@H]1O) `ZINC001341315191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001341315191 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCn2ccnn2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 12, 12, 33, 30, 46, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 33, 33, 36, 36, 42, 43, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315191 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315191/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315191 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 127) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/127 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/127' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCn2ccnn2)C[C@H]1O) `ZINC001341315191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001341315191 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCn2ccnn2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 11, 11, 30, 29, 45, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 30, 30, 35, 35, 41, 42, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315191 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341315191 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315191/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315191/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315191 Building ZINC001341315191 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315191' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315191 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315191 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315191/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315191 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 126) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/126: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCn2ccnn2)C[C@H]1O) `ZINC001341315191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001341315191 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCn2ccnn2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 12, 12, 33, 30, 46, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 33, 33, 36, 36, 42, 43, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315191 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315191/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315191 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 127) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/127: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCn2ccnn2)C[C@H]1O) `ZINC001341315191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001341315191 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCn2ccnn2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 11, 11, 30, 29, 45, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 30, 30, 35, 35, 41, 42, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315191 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341315191 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315191/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315191/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315191 Building ZINC001341315240 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315240' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315240 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315240 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315240/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315240 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/128 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCCCCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341315240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001341315240 none CC(=O)NCCCCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 34, 19, 20, 18, 17, 7, 5, 7, 5, 5, 5, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 33, 34, 20, 20, 19, 20, 20, 20, 17, 17, 5, 5, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315240 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315240/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315240 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 129) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/129 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/129' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCCCCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341315240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001341315240 none CC(=O)NCCCCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 35, 17, 19, 17, 17, 6, 4, 6, 4, 4, 4, 4, 4, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 34, 34, 19, 19, 19, 19, 19, 19, 17, 17, 4, 4, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 150 rigid atoms, others: [51, 50, 54, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 55, 56]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315240 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341315240 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315240/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315240/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315240 Building ZINC001341315240 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315240' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315240 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315240 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315240/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315240 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 128) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/128: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCCCCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341315240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001341315240 none CC(=O)NCCCCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 34, 19, 20, 18, 17, 7, 5, 7, 5, 5, 5, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 33, 34, 20, 20, 19, 20, 20, 20, 17, 17, 5, 5, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315240 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315240/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315240 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 129) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/129: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCCCCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341315240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001341315240 none CC(=O)NCCCCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 35, 17, 19, 17, 17, 6, 4, 6, 4, 4, 4, 4, 4, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 34, 34, 19, 19, 19, 19, 19, 19, 17, 17, 4, 4, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 150 rigid atoms, others: [51, 50, 54, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 25, 26, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 55, 56]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315240 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341315240 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315240/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315240/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315240 Building ZINC001341315249 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315249' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315249 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315249 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315249/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315249 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/130 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@]2(C)CCC(=O)NC2)C[C@H]1O) `ZINC001341315249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341315249 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@]2(C)CCC(=O)NC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 5, 17, 17, 17, 17, 33, 43, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 51] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 188 number of broken/clashed sets: 141 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315249 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315249/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315249 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 131) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/131 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/131' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@]2(C)CCC(=O)NC2)C[C@H]1O) `ZINC001341315249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341315249 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@]2(C)CCC(=O)NC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 18, 18, 18, 18, 35, 43, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 54] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 189 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315249 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341315249 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315249/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315249/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315249 Building ZINC001341315249 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315249' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315249 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315249 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315249/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315249 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 130) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/130: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@]2(C)CCC(=O)NC2)C[C@H]1O) `ZINC001341315249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341315249 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@]2(C)CCC(=O)NC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 5, 17, 17, 17, 17, 33, 43, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 51] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 188 number of broken/clashed sets: 141 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315249 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315249/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315249 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 131) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/131: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@]2(C)CCC(=O)NC2)C[C@H]1O) `ZINC001341315249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341315249 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@]2(C)CCC(=O)NC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 18, 18, 18, 18, 35, 43, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 54] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 189 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315249 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341315249 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315249/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315249/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315249 Building ZINC001341315251 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315251' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315251 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315251 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315251/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315251 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/132 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@]2(C)CCC(=O)NC2)C[C@H]1O) `ZINC001341315251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341315251 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@]2(C)CCC(=O)NC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 32, 43, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 45] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 132 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315251 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315251/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315251 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 133) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/133 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/133' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@]2(C)CCC(=O)NC2)C[C@H]1O) `ZINC001341315251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341315251 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@]2(C)CCC(=O)NC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 30, 41, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 45] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 179 number of broken/clashed sets: 129 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315251 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341315251 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315251/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315251/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315251 Building ZINC001341315251 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315251' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315251 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315251 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315251/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315251 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 132) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/132: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@]2(C)CCC(=O)NC2)C[C@H]1O) `ZINC001341315251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341315251 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@]2(C)CCC(=O)NC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 32, 43, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 45] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 132 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315251 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315251/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315251 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 133) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/133: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@]2(C)CCC(=O)NC2)C[C@H]1O) `ZINC001341315251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001341315251 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@]2(C)CCC(=O)NC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 30, 41, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 45] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 179 number of broken/clashed sets: 129 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315251 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341315251 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315251/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315251/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315251 Building ZINC001341315371 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315371' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315371 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315371 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315371/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315371 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/134 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001341315371.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001341315371 none CC(=O)N1CCC(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 50, 48, 48, 48, 15, 8, 15, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 48, 48, 50, 50, 50, 48, 48, 48, 48, 47, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 48, 48, 48, 48] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 162 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315371 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315371/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315371 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 135) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/135 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/135' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001341315371.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315371/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001341315371 none CC(=O)N1CCC(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 50, 49, 49, 49, 16, 10, 16, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 49, 49, 50, 50, 50, 49, 49, 49, 49, 49, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 49, 49, 49, 49] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 171 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315371 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341315371 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315371/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315371/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315371 Building ZINC001341315371 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315371' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315371 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315371 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315371/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315371 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 134) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/134: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001341315371.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001341315371 none CC(=O)N1CCC(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 50, 48, 48, 48, 15, 8, 15, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 48, 48, 50, 50, 50, 48, 48, 48, 48, 47, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 48, 48, 48, 48] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 162 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315371 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315371/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315371 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 135) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/135: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1) `ZINC001341315371.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315371/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001341315371 none CC(=O)N1CCC(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 50, 49, 49, 49, 16, 10, 16, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 49, 49, 50, 50, 50, 49, 49, 49, 49, 49, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 49, 49, 49, 49] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54]) total number of confs: 171 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315371 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341315371 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315371/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315371/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315371 Building ZINC001341315413 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315413' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315413 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315413 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315413/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315413 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/136 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001341315413.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001341315413 none CCOc1cnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', '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, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 42, 42, 42, 42, 22, 9, 22, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 42, 42, 50, 50, 50, 50, 50, 42, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 42] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315413 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315413/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315413 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 137) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/137 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/137' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001341315413.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315413/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001341315413 none CCOc1cnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', '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, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 44, 44, 44, 44, 25, 12, 25, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 44, 44, 50, 50, 50, 50, 50, 44, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 44] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315413 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341315413 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315413/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315413/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315413 Building ZINC001341315413 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315413' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315413 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315413 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315413/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315413 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 136) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/136: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001341315413.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001341315413 none CCOc1cnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', '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, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 42, 42, 42, 42, 22, 9, 22, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 42, 42, 50, 50, 50, 50, 50, 42, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 42] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315413 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315413/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315413 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 137) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/137: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001341315413.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315413/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001341315413 none CCOc1cnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', '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, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 44, 44, 44, 44, 25, 12, 25, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 44, 44, 50, 50, 50, 50, 50, 44, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 44] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315413 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341315413 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315413/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315413/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315413 Building ZINC001341315898 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315898' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315898 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315898 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315898/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315898 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/138 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccncc1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341315898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001341315898 none COc1ccncc1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 40, 13, 8, 13, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 40, 40, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315898 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315898/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315898 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 139) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/139 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/139' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccncc1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341315898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001341315898 none COc1ccncc1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 39, 12, 8, 12, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 39, 39, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315898 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341315898 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315898/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315898/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315898 Building ZINC001341315898 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315898' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315898 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315898 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315898/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315898 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 138) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/138: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccncc1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341315898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001341315898 none COc1ccncc1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 40, 13, 8, 13, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 40, 40, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315898 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315898/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315898 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 139) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/139: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccncc1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341315898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001341315898 none COc1ccncc1CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 39, 12, 8, 12, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 39, 39, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315898 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341315898 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315898/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315898/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315898 Building ZINC001341315903 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315903' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315903 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315903 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315903/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315903 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/140 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@](C)(C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(C)C) `ZINC001341315903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001341315903 none CC(=O)N[C@@](C)(C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 44, 31, 44, 11, 31, 11, 11, 11, 11, 11, 5, 11, 3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 44, 50, 50, 50, 50, 50, 50, 44, 44, 44, 11, 11, 33, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 253 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315903 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315903/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315903 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 141) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/141 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/141' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@](C)(C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(C)C) `ZINC001341315903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001341315903 none CC(=O)N[C@@](C)(C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 44, 33, 44, 14, 33, 14, 14, 14, 14, 14, 5, 14, 3, 1, 3, 1, 1, 1, 2, 2, 2, 14, 44, 50, 50, 50, 50, 50, 50, 44, 44, 44, 14, 14, 42, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 265 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315903 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341315903 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315903/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315903/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315903 Building ZINC001341315903 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315903' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315903 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315903 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315903/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315903 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 140) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/140: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@](C)(C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(C)C) `ZINC001341315903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001341315903 none CC(=O)N[C@@](C)(C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 44, 31, 44, 11, 31, 11, 11, 11, 11, 11, 5, 11, 3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 44, 50, 50, 50, 50, 50, 50, 44, 44, 44, 11, 11, 33, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 253 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315903 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315903/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315903 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 141) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/141: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@](C)(C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(C)C) `ZINC001341315903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001341315903 none CC(=O)N[C@@](C)(C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 44, 33, 44, 14, 33, 14, 14, 14, 14, 14, 5, 14, 3, 1, 3, 1, 1, 1, 2, 2, 2, 14, 44, 50, 50, 50, 50, 50, 50, 44, 44, 44, 14, 14, 42, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 265 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315903 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341315903 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315903/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315903/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315903 Building ZINC001341315904 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315904' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315904 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315904 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315904/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315904 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/142 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@](C)(C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(C)C) `ZINC001341315904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001341315904 none CC(=O)N[C@](C)(C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 46, 34, 46, 10, 34, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 2, 2, 2, 10, 46, 50, 50, 50, 50, 50, 50, 46, 46, 46, 10, 10, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 239 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315904 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315904/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315904 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 143) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/143 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/143' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@](C)(C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(C)C) `ZINC001341315904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001341315904 none CC(=O)N[C@](C)(C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 47, 36, 47, 12, 36, 12, 12, 12, 12, 12, 5, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 47, 50, 50, 50, 50, 50, 50, 47, 47, 47, 12, 12, 36, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 229 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315904 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341315904 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315904/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315904/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315904 Building ZINC001341315904 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315904' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315904 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341315904 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315904/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315904 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 142) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/142: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@](C)(C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(C)C) `ZINC001341315904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341315904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001341315904 none CC(=O)N[C@](C)(C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 46, 34, 46, 10, 34, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 2, 2, 2, 10, 46, 50, 50, 50, 50, 50, 50, 46, 46, 46, 10, 10, 30, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 239 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315904 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315904/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315904 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 143) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/143: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@](C)(C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(C)C) `ZINC001341315904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341315904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001341315904 none CC(=O)N[C@](C)(C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 47, 36, 47, 12, 36, 12, 12, 12, 12, 12, 5, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 47, 50, 50, 50, 50, 50, 50, 47, 47, 47, 12, 12, 36, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 229 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315904 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341315904 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315904/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315904/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341315904 Building ZINC001341316036 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316036' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316036 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341316036 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316036/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316036 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/144 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341316036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341316036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341316036 none CN1C(=O)CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 29, 50, 12, 29, 12, 12, 12, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 187 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316036 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316036/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316036 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 145) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/145 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/145' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341316036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341316036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341316036 none CN1C(=O)CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 13, 31, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 192 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316036 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341316036 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316036/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316036/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316036 Building ZINC001341316036 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316036' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316036 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341316036 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316036/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316036 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 144) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/144: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341316036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341316036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341316036 none CN1C(=O)CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 29, 50, 12, 29, 12, 12, 12, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 187 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316036 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316036/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316036 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 145) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/145: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341316036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341316036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341316036 none CN1C(=O)CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 13, 31, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 192 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316036 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341316036 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316036/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316036/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316036 Building ZINC001341316038 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316038' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316038 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341316038 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316038/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316038 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/146 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341316038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341316038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341316038 none CN1C(=O)CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 13, 31, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 190 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316038 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316038/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316038 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 147) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/147 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/147' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341316038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341316038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341316038 none CN1C(=O)CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 29, 50, 12, 29, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 191 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316038 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341316038 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316038/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316038/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316038 Building ZINC001341316038 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316038' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316038 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341316038 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316038/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316038 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 146) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/146: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341316038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341316038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341316038 none CN1C(=O)CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 13, 31, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 190 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316038 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316038/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316038 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 147) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/147: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341316038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341316038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001341316038 none CN1C(=O)CCC[C@@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 29, 50, 12, 29, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 191 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316038 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341316038 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316038/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316038/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316038 Building ZINC001341316057 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316057' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316057 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341316057 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316057/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316057 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/148 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCn2cncn2)C[C@H]1O) `ZINC001341316057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341316057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001341316057 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCn2cncn2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 8, 1, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 10, 10, 33, 28, 43, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 33, 33, 34, 34, 39, 40, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316057 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316057/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316057 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 149) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/149 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/149' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCn2cncn2)C[C@H]1O) `ZINC001341316057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341316057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001341316057 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCn2cncn2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 8, 1, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 10, 10, 28, 26, 43, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 28, 28, 34, 34, 39, 39, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316057 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341316057 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316057/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316057/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316057 Building ZINC001341316057 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316057' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316057 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341316057 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316057/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316057 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 148) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/148: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCn2cncn2)C[C@H]1O) `ZINC001341316057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341316057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001341316057 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCn2cncn2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 8, 1, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 10, 10, 33, 28, 43, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 33, 33, 34, 34, 39, 40, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316057 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316057/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316057 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 149) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/149: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCn2cncn2)C[C@H]1O) `ZINC001341316057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341316057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001341316057 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCn2cncn2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 8, 1, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 10, 10, 28, 26, 43, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 28, 28, 34, 34, 39, 39, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316057 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341316057 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316057/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316057/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316057 Building ZINC001341316401 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316401' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316401 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341316401 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316401/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316401 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/150 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341316401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341316401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341316401 none CC(=O)N(C)CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 44, 50, 32, 33, 15, 10, 15, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 41, 44, 35, 35, 33, 33, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 253 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316401 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316401/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316401 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 151) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/151 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/151' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341316401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341316401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341316401 none CC(=O)N(C)CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 42, 50, 34, 34, 16, 9, 16, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 40, 42, 36, 36, 34, 34, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 244 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316401 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341316401 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316401/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316401/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316401 Building ZINC001341316401 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316401' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316401 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341316401 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316401/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316401 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 150) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/150: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341316401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341316401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341316401 none CC(=O)N(C)CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 44, 50, 32, 33, 15, 10, 15, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 41, 44, 35, 35, 33, 33, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 253 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316401 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316401/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316401 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 151) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/151: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341316401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341316401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341316401 none CC(=O)N(C)CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 42, 50, 34, 34, 16, 9, 16, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 40, 42, 36, 36, 34, 34, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53]) total number of confs: 244 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316401 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341316401 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316401/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316401/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316401 Building ZINC001341316426 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316426' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316426 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341316426 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316426/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316426 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/152 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001341316426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341316426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001341316426 none Cc1noc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 20, 20, 10, 6, 10, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 20, 20, 20, 20, 6, 6, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316426 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316426/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316426 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 153) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/153 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/153' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001341316426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341316426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001341316426 none Cc1noc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 23, 21, 13, 9, 13, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 23, 23, 21, 21, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316426 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341316426 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316426/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316426/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316426 Building ZINC001341316426 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316426' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316426 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341316426 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316426/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316426 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 152) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/152: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001341316426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341316426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001341316426 none Cc1noc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 20, 20, 10, 6, 10, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 20, 20, 20, 20, 6, 6, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316426 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316426/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316426 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 153) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/153: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001341316426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341316426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001341316426 none Cc1noc(CCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 23, 21, 13, 9, 13, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 23, 23, 21, 21, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316426 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341316426 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316426/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316426/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341316426 Building ZINC001341317606 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317606' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317606 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341317606 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317606/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317606 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/154 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3nncn3C2)C[C@H]1O) `ZINC001341317606.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341317606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001341317606 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3nncn3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 23, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317606 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317606/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317606 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 155) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/155 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/155' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3nncn3C2)C[C@H]1O) `ZINC001341317606.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341317606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001341317606 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3nncn3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 23, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 163 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317606 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341317606 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317606/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317606/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317606 Building ZINC001341317606 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317606' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317606 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341317606 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317606/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317606 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 154) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/154: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3nncn3C2)C[C@H]1O) `ZINC001341317606.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341317606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001341317606 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3nncn3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 23, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317606 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317606/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317606 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 155) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/155: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3nncn3C2)C[C@H]1O) `ZINC001341317606.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341317606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001341317606 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3nncn3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 23, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 163 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317606 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341317606 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317606/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317606/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317606 Building ZINC001341317609 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317609' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317609 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341317609 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317609/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317609 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/156 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3nncn3C2)C[C@H]1O) `ZINC001341317609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341317609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001341317609 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3nncn3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 25, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 171 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317609 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317609/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317609 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 157) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/157 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/157' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3nncn3C2)C[C@H]1O) `ZINC001341317609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341317609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001341317609 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3nncn3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 25, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 165 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317609 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341317609 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317609/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317609/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317609 Building ZINC001341317609 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317609' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317609 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341317609 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317609/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317609 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 156) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/156: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3nncn3C2)C[C@H]1O) `ZINC001341317609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341317609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001341317609 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3nncn3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 25, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 171 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317609 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317609/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317609 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 157) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/157: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3nncn3C2)C[C@H]1O) `ZINC001341317609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341317609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001341317609 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3nncn3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 25, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 165 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317609 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341317609 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317609/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317609/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317609 Building ZINC001341317681 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317681' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317681 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341317681 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317681/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317681 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/158 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1nocc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341317681.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341317681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001341317681 none COCc1nocc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 34, 34, 34, 34, 34, 14, 8, 14, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 34, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317681 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317681/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317681 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 159) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/159 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/159' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1nocc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341317681.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341317681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317681/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001341317681 none COCc1nocc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 32, 32, 32, 32, 32, 14, 7, 14, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 32, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317681 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341317681 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317681/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317681/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317681 Building ZINC001341317681 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317681' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317681 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341317681 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317681/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317681 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 158) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/158: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1nocc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341317681.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341317681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001341317681 none COCc1nocc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 34, 34, 34, 34, 34, 14, 8, 14, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 34, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317681 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317681/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317681 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 159) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/159: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1nocc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341317681.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341317681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317681/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001341317681 none COCc1nocc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 32, 32, 32, 32, 32, 14, 7, 14, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 32, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317681 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341317681 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317681/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317681/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341317681 Building ZINC001341318113 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318113' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318113 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341318113 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318113/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318113 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/160 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCn2ccccc2=O)C[C@H]1O) `ZINC001341318113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341318113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001341318113 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCn2ccccc2=O)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 17, 17, 40, 41, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 40, 40, 41, 41, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318113 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318113/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318113 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 161) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/161 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/161' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCn2ccccc2=O)C[C@H]1O) `ZINC001341318113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341318113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001341318113 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCn2ccccc2=O)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 18, 18, 37, 39, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 37, 37, 39, 39, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318113 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341318113 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318113/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318113/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318113 Building ZINC001341318113 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318113' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318113 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341318113 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318113/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318113 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 160) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/160: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCn2ccccc2=O)C[C@H]1O) `ZINC001341318113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341318113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001341318113 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCn2ccccc2=O)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 17, 17, 40, 41, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 40, 40, 41, 41, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318113 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318113/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318113 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 161) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/161: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCn2ccccc2=O)C[C@H]1O) `ZINC001341318113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341318113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001341318113 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCn2ccccc2=O)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 18, 18, 37, 39, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 37, 37, 39, 39, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318113 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341318113 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318113/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318113/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318113 Building ZINC001341318162 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318162' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318162 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341318162 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318162/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318162 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/162 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341318162.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341318162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341318162 none CNC(=O)CCCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 40, 50, 27, 25, 23, 9, 6, 9, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 40, 40, 27, 27, 27, 27, 23, 23, 6, 6, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [51, 50, 49, 42, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 246 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318162 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318162/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318162 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 163) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/163 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/163' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341318162.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341318162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341318162 none CNC(=O)CCCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 41, 50, 26, 24, 20, 7, 5, 7, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 41, 41, 26, 26, 26, 26, 20, 20, 5, 5, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 150 rigid atoms, others: [51, 50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25, 47] 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, 52, 53]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318162 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341318162 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318162/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318162/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318162 Building ZINC001341318162 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318162' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318162 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341318162 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318162/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318162 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 162) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/162: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341318162.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341318162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341318162 none CNC(=O)CCCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 40, 50, 27, 25, 23, 9, 6, 9, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 40, 40, 27, 27, 27, 27, 23, 23, 6, 6, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [51, 50, 49, 42, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 52, 53]) total number of confs: 246 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318162 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318162/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318162 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 163) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/163: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341318162.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341318162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341318162 none CNC(=O)CCCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 41, 50, 26, 24, 20, 7, 5, 7, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 41, 41, 26, 26, 26, 26, 20, 20, 5, 5, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 150 rigid atoms, others: [51, 50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25, 47] 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, 52, 53]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318162 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341318162 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318162/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318162/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318162 Building ZINC001341318492 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318492' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318492 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341318492 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318492/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318492 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/164 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(O)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1C) `ZINC001341318492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341318492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001341318492 none Cc1nnc(O)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 12, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 5, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 31, 11, 31, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 100, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50] 300 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318492 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318492/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318492 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 165) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/165 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/165' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(O)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1C) `ZINC001341318492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341318492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001341318492 none Cc1nnc(O)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 12, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 5, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 31, 10, 31, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 100, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50] 300 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318492 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341318492 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318492/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318492/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318492 Building ZINC001341318492 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318492' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318492 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341318492 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318492/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318492 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 164) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/164: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(O)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1C) `ZINC001341318492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341318492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001341318492 none Cc1nnc(O)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 12, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 5, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 31, 11, 31, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 100, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50] 300 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318492 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318492/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318492 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 165) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/165: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(O)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1C) `ZINC001341318492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341318492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001341318492 none Cc1nnc(O)c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 12, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 5, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 31, 10, 31, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 100, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50] 300 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318492 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341318492 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318492/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318492/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318492 Building ZINC001341318496 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318496' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318496 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341318496 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318496/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318496 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/166 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H](CC(C)C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341318496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341318496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001341318496 none CC(=O)N[C@@H](CC(C)C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 30, 50, 50, 50, 50, 50, 12, 30, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 217 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318496 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318496/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318496 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 167) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/167 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/167' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H](CC(C)C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341318496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341318496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001341318496 none CC(=O)N[C@@H](CC(C)C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 49, 26, 49, 49, 50, 50, 50, 10, 26, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 227 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318496 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341318496 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318496/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318496/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318496 Building ZINC001341318496 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318496' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318496 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341318496 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318496/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318496 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 166) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H](CC(C)C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341318496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341318496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001341318496 none CC(=O)N[C@@H](CC(C)C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 30, 50, 50, 50, 50, 50, 12, 30, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 217 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318496 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318496/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318496 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 167) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/167: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H](CC(C)C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001341318496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341318496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001341318496 none CC(=O)N[C@@H](CC(C)C)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 49, 26, 49, 49, 50, 50, 50, 10, 26, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 227 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318496 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341318496 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318496/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318496/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318496 Building ZINC001341318597 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318597' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318597 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341318597 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318597/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318597 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/168 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@@](C)(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001341318597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341318597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001341318597 none CC(=O)N1CC[C@@](C)(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 31, 50, 31, 31, 31, 25, 31, 9, 25, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 2, 2, 2, 9, 31, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 9, 9, 27, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 31, 31] 150 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 202 number of broken/clashed sets: 102 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318597 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318597/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318597 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 169) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/169 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/169' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@@](C)(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001341318597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341318597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001341318597 none CC(=O)N1CC[C@@](C)(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 29, 50, 29, 29, 29, 24, 29, 9, 24, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 29, 50, 50, 50, 29, 29, 29, 29, 29, 29, 29, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 29, 29] 150 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: 196 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318597 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341318597 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318597/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318597/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318597 Building ZINC001341318597 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318597' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318597 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341318597 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318597/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318597 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 168) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/168: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@@](C)(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001341318597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341318597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001341318597 none CC(=O)N1CC[C@@](C)(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 31, 50, 31, 31, 31, 25, 31, 9, 25, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 2, 2, 2, 9, 31, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 9, 9, 27, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 31, 31] 150 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 202 number of broken/clashed sets: 102 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318597 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318597/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318597 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 169) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/169: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@@](C)(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001341318597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341318597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001341318597 none CC(=O)N1CC[C@@](C)(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 29, 50, 29, 29, 29, 24, 29, 9, 24, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 29, 50, 50, 50, 29, 29, 29, 29, 29, 29, 29, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 29, 29] 150 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: 196 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318597 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341318597 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318597/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318597/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318597 Building ZINC001341318599 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318599' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318599 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341318599 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318599/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318599 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/170 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@](C)(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001341318599.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341318599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001341318599 none CC(=O)N1CC[C@](C)(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 37, 50, 37, 37, 37, 28, 37, 9, 28, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 2, 2, 2, 9, 37, 50, 50, 50, 37, 37, 37, 37, 37, 37, 37, 9, 9, 27, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 37, 37] 150 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 196 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318599 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318599/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318599 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 171) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/171 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/171' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@](C)(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001341318599.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341318599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318599/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001341318599 none CC(=O)N1CC[C@](C)(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 36, 50, 36, 36, 36, 27, 36, 8, 27, 8, 8, 8, 8, 8, 4, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 36, 50, 50, 50, 36, 36, 36, 36, 36, 36, 36, 8, 8, 24, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 36, 36] 150 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: 183 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318599 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341318599 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318599/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318599/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318599 Building ZINC001341318599 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318599' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318599 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341318599 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318599/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318599 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 170) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/170: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@](C)(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001341318599.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341318599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001341318599 none CC(=O)N1CC[C@](C)(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 37, 50, 37, 37, 37, 28, 37, 9, 28, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 2, 2, 2, 9, 37, 50, 50, 50, 37, 37, 37, 37, 37, 37, 37, 9, 9, 27, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 37, 37] 150 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 196 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318599 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318599/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318599 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 171) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/171: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@](C)(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001341318599.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341318599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318599/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001341318599 none CC(=O)N1CC[C@](C)(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 36, 50, 36, 36, 36, 27, 36, 8, 27, 8, 8, 8, 8, 8, 4, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 36, 50, 50, 50, 36, 36, 36, 36, 36, 36, 36, 8, 8, 24, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 36, 36] 150 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: 183 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318599 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341318599 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318599/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318599/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318599 Building ZINC001341318665 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001341318665 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/172 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O) `ZINC001341318665.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341318665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341318665 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 23, 28, 28, 28, 44, 44, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 84] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 211 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 173) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/173 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/173' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O) `ZINC001341318665.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341318665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341318665 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 5, 23, 28, 28, 28, 45, 45, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 84] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 218 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 174) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/174 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/174' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O) `ZINC001341318665.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001341318665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341318665 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 23, 28, 28, 28, 44, 44, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 84] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 211 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 175) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/175 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/175' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O) `ZINC001341318665.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001341318665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341318665 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 5, 23, 28, 28, 28, 45, 45, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 84] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 218 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341318665 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 Building ZINC001341318665 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001341318665 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 172) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/172: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O) `ZINC001341318665.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341318665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341318665 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 23, 28, 28, 28, 44, 44, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 84] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 211 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 173) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/173: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O) `ZINC001341318665.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341318665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341318665 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 5, 23, 28, 28, 28, 45, 45, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 84] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 218 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 174) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/174: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O) `ZINC001341318665.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001341318665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341318665 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 23, 28, 28, 28, 44, 44, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 84] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 211 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 175) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/175: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O) `ZINC001341318665.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001341318665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341318665 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 5, 23, 28, 28, 28, 45, 45, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 84] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 218 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341318665 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 Building ZINC001341318665 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001341318665 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 172) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/172: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O) `ZINC001341318665.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341318665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341318665 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 23, 28, 28, 28, 44, 44, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 84] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 211 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 173) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/173: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O) `ZINC001341318665.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341318665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341318665 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 5, 23, 28, 28, 28, 45, 45, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 84] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 218 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 174) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/174: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O) `ZINC001341318665.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001341318665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341318665 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 23, 28, 28, 28, 44, 44, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 84] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 211 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 175) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/175: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O) `ZINC001341318665.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001341318665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341318665 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 5, 23, 28, 28, 28, 45, 45, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 84] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 218 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341318665 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 Building ZINC001341318665 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001341318665 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 172) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/172: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O) `ZINC001341318665.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341318665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341318665 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 23, 28, 28, 28, 44, 44, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 84] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 211 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 173) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/173: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O) `ZINC001341318665.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341318665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341318665 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 5, 23, 28, 28, 28, 45, 45, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 84] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 218 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 174) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/174: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O) `ZINC001341318665.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001341318665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341318665 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 23, 28, 28, 28, 44, 44, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 84] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 211 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 175) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/175: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O) `ZINC001341318665.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001341318665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341318665 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C23CCCN2CCC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 5, 23, 28, 28, 28, 45, 45, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 84] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 218 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341318665 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318665 Building ZINC001341318822 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318822' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318822 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341318822 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318822/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318822 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/176 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccn(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1=O) `ZINC001341318822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341318822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001341318822 none Cc1cccn(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 38, 12, 7, 12, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318822 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318822/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318822 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 177) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/177 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/177' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccn(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1=O) `ZINC001341318822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341318822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001341318822 none Cc1cccn(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 40, 12, 6, 12, 6, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 6, 6, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 180 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318822 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341318822 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318822/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318822/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318822 Building ZINC001341318822 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318822' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318822 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341318822 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318822/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318822 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 176) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/176: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccn(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1=O) `ZINC001341318822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341318822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001341318822 none Cc1cccn(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 38, 12, 7, 12, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318822 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318822/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318822 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 177) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/177: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccn(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1=O) `ZINC001341318822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341318822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001341318822 none Cc1cccn(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 40, 12, 6, 12, 6, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 6, 6, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 180 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318822 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341318822 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318822/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318822/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341318822 Building ZINC001341563920 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563920' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563920 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341563920 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563920/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563920 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/178 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](C(N)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001341563920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341563920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341563920 none CC(C)C[C@H](C(N)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 40, 40, 40, 17, 40, 40, 50, 50, 17, 17, 6, 6, 6, 6, 4, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 40, 40, 40, 40, 40, 40, 40, 40, 40, 50, 50, 17, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 205 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563920 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563920/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563920 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 179) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/179 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/179' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](C(N)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001341563920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341563920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341563920 none CC(C)C[C@H](C(N)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 38, 17, 38, 38, 50, 50, 17, 17, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 38, 38, 38, 38, 38, 38, 38, 38, 38, 50, 50, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 211 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563920 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341563920 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563920/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563920/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563920 Building ZINC001341563920 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563920' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563920 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341563920 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563920/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563920 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 178) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/178: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](C(N)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001341563920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341563920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341563920 none CC(C)C[C@H](C(N)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 40, 40, 40, 17, 40, 40, 50, 50, 17, 17, 6, 6, 6, 6, 4, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 40, 40, 40, 40, 40, 40, 40, 40, 40, 50, 50, 17, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 205 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563920 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563920/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563920 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 179) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/179: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](C(N)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001341563920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341563920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341563920 none CC(C)C[C@H](C(N)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 38, 17, 38, 38, 50, 50, 17, 17, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 38, 38, 38, 38, 38, 38, 38, 38, 38, 50, 50, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 211 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563920 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341563920 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563920/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563920/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563920 Building ZINC001341563927 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563927' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563927 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341563927 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563927/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563927 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/180 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H](C(N)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001341563927.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341563927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341563927 none CC(C)C[C@@H](C(N)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 46, 18, 46, 46, 49, 49, 18, 18, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 208 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563927 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563927/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563927 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 181) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/181 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/181' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H](C(N)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001341563927.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341563927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341563927 none CC(C)C[C@@H](C(N)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 42, 42, 41, 15, 41, 41, 50, 50, 15, 15, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 42, 42, 42, 42, 42, 42, 42, 42, 42, 50, 50, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 202 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563927 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341563927 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563927/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563927/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563927 Building ZINC001341563927 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563927' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563927 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341563927 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563927/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563927 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 180) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/180: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H](C(N)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001341563927.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341563927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341563927 none CC(C)C[C@@H](C(N)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 46, 18, 46, 46, 49, 49, 18, 18, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 208 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563927 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563927/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563927 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 181) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/181: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H](C(N)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001341563927.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341563927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341563927 none CC(C)C[C@@H](C(N)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 42, 42, 41, 15, 41, 41, 50, 50, 15, 15, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 42, 42, 42, 42, 42, 42, 42, 42, 42, 50, 50, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 202 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563927 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341563927 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563927/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563927/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341563927 Building ZINC001341589230 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341589230' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341589230 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341589230 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341589230/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341589230 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/182 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(C)(C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001341589230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341589230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341589230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341589230 none CC(=O)NCC(C)(C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 39, 31, 14, 31, 31, 14, 14, 9, 9, 9, 9, 4, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 39, 39, 31, 31, 31, 31, 31, 31, 14, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 27] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341589230 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341589230/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341589230 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 183) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/183 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/183' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(C)(C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001341589230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341589230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341589230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341589230 none CC(=O)NCC(C)(C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 43, 30, 12, 30, 30, 12, 12, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 43, 43, 30, 30, 30, 30, 30, 30, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341589230 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341589230 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341589230/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341589230/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341589230 Building ZINC001341589230 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341589230' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341589230 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341589230 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341589230/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341589230 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 182) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/182: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(C)(C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001341589230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341589230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341589230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341589230 none CC(=O)NCC(C)(C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 39, 31, 14, 31, 31, 14, 14, 9, 9, 9, 9, 4, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 39, 39, 31, 31, 31, 31, 31, 31, 14, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 27] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341589230 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341589230/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341589230 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 183) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/183: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(C)(C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001341589230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341589230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341589230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001341589230 none CC(=O)NCC(C)(C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 43, 30, 12, 30, 30, 12, 12, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 43, 43, 30, 30, 30, 30, 30, 30, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341589230 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341589230 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341589230/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341589230/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341589230 Building ZINC001341668752 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668752' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668752 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341668752 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668752/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668752 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/184 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)C(C)(C)C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001341668752.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341668752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001341668752 none C[C@@H](NC(=O)C(C)(C)C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 19, 44, 44, 50, 50, 50, 50, 50, 50, 19, 19, 10, 10, 10, 10, 6, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 30] 150 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668752 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668752/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668752 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 185) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/185 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/185' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)C(C)(C)C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001341668752.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341668752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668752/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001341668752 none C[C@@H](NC(=O)C(C)(C)C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 15, 44, 44, 50, 50, 50, 50, 50, 50, 15, 15, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668752 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341668752 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668752/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668752/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668752 Building ZINC001341668752 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668752' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668752 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341668752 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668752/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668752 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 184) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/184: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)C(C)(C)C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001341668752.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341668752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001341668752 none C[C@@H](NC(=O)C(C)(C)C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 19, 44, 44, 50, 50, 50, 50, 50, 50, 19, 19, 10, 10, 10, 10, 6, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 30] 150 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668752 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668752/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668752 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 185) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/185: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)C(C)(C)C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001341668752.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341668752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668752/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001341668752 none C[C@@H](NC(=O)C(C)(C)C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 15, 44, 44, 50, 50, 50, 50, 50, 50, 15, 15, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668752 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341668752 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668752/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668752/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668752 Building ZINC001341668753 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668753' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668753 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341668753 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668753/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668753 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/186 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C(C)(C)C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001341668753.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341668753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001341668753 none C[C@H](NC(=O)C(C)(C)C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 17, 44, 44, 50, 50, 50, 50, 50, 50, 17, 17, 9, 9, 9, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 27] 150 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668753 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668753/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668753 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 187) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/187 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/187' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C(C)(C)C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001341668753.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341668753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668753/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001341668753 none C[C@H](NC(=O)C(C)(C)C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [43, 14, 43, 43, 50, 50, 50, 50, 50, 50, 14, 14, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 197 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668753 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341668753 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668753/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668753/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668753 Building ZINC001341668753 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668753' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668753 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001341668753 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668753/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668753 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 186) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/186: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C(C)(C)C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001341668753.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001341668753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001341668753 none C[C@H](NC(=O)C(C)(C)C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 17, 44, 44, 50, 50, 50, 50, 50, 50, 17, 17, 9, 9, 9, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 27] 150 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668753 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668753/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668753 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 187) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/187: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)C(C)(C)C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001341668753.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001341668753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668753/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001341668753 none C[C@H](NC(=O)C(C)(C)C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [43, 14, 43, 43, 50, 50, 50, 50, 50, 50, 14, 14, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 197 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668753 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001341668753 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668753/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668753/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001341668753 Building ZINC001342289527 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342289527' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342289527 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342289527 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342289527/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342289527 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/188 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CN(C)S(C)(=O)=O) `ZINC001342289527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342289527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342289527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001342289527 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CN(C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 16, 16, 16, 40, 49, 49, 50, 50, 50, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 16, 40, 40, 49, 49, 49, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342289527 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342289527/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342289527 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 189) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/189 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/189' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CN(C)S(C)(=O)=O) `ZINC001342289527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342289527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342289527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001342289527 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CN(C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 13, 13, 42, 49, 49, 50, 50, 50, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 42, 42, 49, 49, 49, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342289527 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001342289527 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342289527/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342289527/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342289527 Building ZINC001342289527 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342289527' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342289527 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342289527 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342289527/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342289527 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 188) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/188: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CN(C)S(C)(=O)=O) `ZINC001342289527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342289527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342289527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001342289527 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CN(C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 16, 16, 16, 40, 49, 49, 50, 50, 50, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 16, 40, 40, 49, 49, 49, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342289527 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342289527/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342289527 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 189) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/189: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CN(C)S(C)(=O)=O) `ZINC001342289527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342289527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342289527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001342289527 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CN(C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 13, 13, 42, 49, 49, 50, 50, 50, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 42, 42, 49, 49, 49, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342289527 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001342289527 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342289527/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342289527/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342289527 Building ZINC001342810230 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342810230' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342810230 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342810230 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342810230/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342810230 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/190 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2ccc(O)nn2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342810230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342810230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342810230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001342810230 none CO[C@@H]1CN(C(=O)c2ccc(O)nn2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 3, 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] 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, 15, 15, 15, 15, 15, 15, 31, 31, 50, 50, 50, 50, 50, 50, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 15, 15, 50, 50, 100, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342810230 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342810230/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342810230 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 191) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/191 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/191' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2ccc(O)nn2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342810230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342810230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342810230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001342810230 none CO[C@@H]1CN(C(=O)c2ccc(O)nn2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 3, 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] 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: [18, 11, 11, 11, 11, 11, 11, 26, 26, 50, 50, 50, 50, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 11, 11, 50, 50, 100, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342810230 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001342810230 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342810230/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342810230/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342810230 Building ZINC001342810230 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342810230' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342810230 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342810230 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342810230/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342810230 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 190) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/190: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2ccc(O)nn2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342810230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342810230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342810230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001342810230 none CO[C@@H]1CN(C(=O)c2ccc(O)nn2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 3, 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] 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, 15, 15, 15, 15, 15, 15, 31, 31, 50, 50, 50, 50, 50, 50, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 15, 15, 50, 50, 100, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342810230 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342810230/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342810230 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 191) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/191: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2ccc(O)nn2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342810230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342810230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342810230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001342810230 none CO[C@@H]1CN(C(=O)c2ccc(O)nn2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 3, 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] 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: [18, 11, 11, 11, 11, 11, 11, 26, 26, 50, 50, 50, 50, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 11, 11, 50, 50, 100, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342810230 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001342810230 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342810230/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342810230/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342810230 Building ZINC001342811764 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811764' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811764 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342811764 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811764/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811764 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/192 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2ccc(=O)n(C)c2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342811764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342811764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001342811764 none CO[C@@H]1CN(C(=O)c2ccc(=O)n(C)c2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 11, 11, 11, 11, 11, 11, 26, 26, 50, 50, 50, 50, 50, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 11, 11, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811764 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811764/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811764 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 193) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/193 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/193' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2ccc(=O)n(C)c2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342811764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342811764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001342811764 none CO[C@@H]1CN(C(=O)c2ccc(=O)n(C)c2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 10, 10, 10, 10, 10, 25, 25, 50, 50, 50, 50, 50, 50, 50, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 10, 10, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811764 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001342811764 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811764/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811764/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811764 Building ZINC001342811764 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811764' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811764 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342811764 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811764/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811764 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 192) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/192: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2ccc(=O)n(C)c2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342811764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342811764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001342811764 none CO[C@@H]1CN(C(=O)c2ccc(=O)n(C)c2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 11, 11, 11, 11, 11, 11, 26, 26, 50, 50, 50, 50, 50, 50, 50, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 11, 11, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811764 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811764/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811764 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 193) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/193: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2ccc(=O)n(C)c2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342811764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342811764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001342811764 none CO[C@@H]1CN(C(=O)c2ccc(=O)n(C)c2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 10, 10, 10, 10, 10, 25, 25, 50, 50, 50, 50, 50, 50, 50, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 10, 10, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811764 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001342811764 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811764/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811764/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811764 Building ZINC001342811877 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811877' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811877 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342811877 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811877/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811877 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/194 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)CNC(=O)C2CC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342811877.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342811877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001342811877 none CO[C@@H]1CN(C(=O)CNC(=O)C2CC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 13, 13, 24, 34, 34, 34, 50, 50, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 7, 7, 24, 24, 34, 50, 50, 50, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811877 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811877/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811877 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 195) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/195 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/195' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)CNC(=O)C2CC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342811877.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342811877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001342811877 none CO[C@@H]1CN(C(=O)CNC(=O)C2CC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 10, 10, 10, 10, 10, 16, 16, 28, 35, 35, 35, 50, 50, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 10, 10, 28, 28, 35, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811877 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001342811877 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811877/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811877/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811877 Building ZINC001342811877 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811877' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811877 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342811877 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811877/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811877 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 194) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/194: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)CNC(=O)C2CC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001342811877.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342811877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001342811877 none CO[C@@H]1CN(C(=O)CNC(=O)C2CC2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 13, 13, 24, 34, 34, 34, 50, 50, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 7, 7, 24, 24, 34, 50, 50, 50, 50, 50, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811877 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811877/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811877 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 195) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/195: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)CNC(=O)C2CC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001342811877.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342811877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001342811877 none CO[C@@H]1CN(C(=O)CNC(=O)C2CC2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 10, 10, 10, 10, 10, 16, 16, 28, 35, 35, 35, 50, 50, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 10, 10, 28, 28, 35, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811877 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001342811877 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811877/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811877/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342811877 Building ZINC001342812280 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342812280' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342812280 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342812280 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342812280/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342812280 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/196 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)CC1) `ZINC001342812280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342812280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342812280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001342812280 none CNC(=O)C1(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 50, 35, 12, 35, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 17, 12, 45, 45, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 12, 12, 45, 45, 45, 45] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342812280 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342812280/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342812280 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 197) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/197 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/197' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)CC1) `ZINC001342812280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342812280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342812280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001342812280 none CNC(=O)C1(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 50, 33, 13, 33, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 19, 13, 43, 43, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 13, 13, 43, 43, 43, 43] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 170 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342812280 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001342812280 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342812280/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342812280/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342812280 Building ZINC001342812280 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342812280' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342812280 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342812280 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342812280/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342812280 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 196) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/196: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)CC1) `ZINC001342812280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342812280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342812280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001342812280 none CNC(=O)C1(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 50, 35, 12, 35, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 17, 12, 45, 45, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 12, 12, 45, 45, 45, 45] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 164 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342812280 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342812280/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342812280 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 197) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/197: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)CC1) `ZINC001342812280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342812280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342812280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001342812280 none CNC(=O)C1(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 50, 33, 13, 33, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 19, 13, 43, 43, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 13, 13, 43, 43, 43, 43] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 170 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342812280 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001342812280 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342812280/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342812280/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342812280 Building ZINC001342919988 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342919988' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342919988 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342919988 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342919988/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342919988 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/198 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001342919988.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342919988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342919988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001342919988 none COCC(=O)NCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 35, 35, 35, 23, 21, 10, 10, 10, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 10, 50, 50, 50, 50, 50, 35, 23, 23, 21, 21, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342919988 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342919988/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342919988 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 199) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/199 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/199' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001342919988.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342919988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342919988/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001342919988 none COCC(=O)NCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 35, 35, 35, 22, 18, 7, 7, 7, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 6, 50, 50, 50, 50, 50, 35, 22, 22, 18, 18, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342919988 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001342919988 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342919988/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342919988/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342919988 Building ZINC001342919988 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342919988' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342919988 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342919988 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342919988/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342919988 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 198) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/198: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001342919988.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342919988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342919988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001342919988 none COCC(=O)NCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 35, 35, 35, 23, 21, 10, 10, 10, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 10, 50, 50, 50, 50, 50, 35, 23, 23, 21, 21, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342919988 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342919988/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342919988 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 199) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/199: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)NCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001342919988.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342919988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342919988/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001342919988 none COCC(=O)NCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 35, 35, 35, 22, 18, 7, 7, 7, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 6, 50, 50, 50, 50, 50, 35, 22, 22, 18, 18, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342919988 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001342919988 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342919988/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342919988/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342919988 Building ZINC001342920762 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342920762' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342920762 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342920762 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342920762/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342920762 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/200 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N(C)CC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001342920762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342920762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342920762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001342920762 none COCC(=O)N(C)CC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 35, 35, 34, 35, 14, 14, 14, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 50, 50, 50, 50, 50, 35, 35, 35, 34, 34, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 6] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342920762 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342920762/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342920762 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 201) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/201 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/201' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N(C)CC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001342920762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342920762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342920762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001342920762 none COCC(=O)N(C)CC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 32, 32, 29, 32, 8, 8, 8, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 5, 50, 50, 50, 50, 50, 32, 32, 32, 29, 29, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342920762 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001342920762 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342920762/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342920762/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342920762 Building ZINC001342920762 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342920762' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342920762 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342920762 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342920762/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342920762 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 200) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/200: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N(C)CC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001342920762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342920762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342920762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001342920762 none COCC(=O)N(C)CC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 35, 35, 34, 35, 14, 14, 14, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 50, 50, 50, 50, 50, 35, 35, 35, 34, 34, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 6] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342920762 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342920762/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342920762 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 201) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/201: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N(C)CC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001342920762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342920762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342920762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001342920762 none COCC(=O)N(C)CC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 32, 32, 29, 32, 8, 8, 8, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 5, 50, 50, 50, 50, 50, 32, 32, 32, 29, 29, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342920762 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001342920762 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342920762/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342920762/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342920762 Building ZINC001342965474 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342965474' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342965474 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342965474 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342965474/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342965474 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/202 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C(=O)NCC(F)F) `ZINC001342965474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342965474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342965474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001342965474 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C(=O)NCC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 11, 8, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 18, 18, 18, 48, 50, 50, 8, 8, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 18, 48, 48, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342965474 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342965474/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342965474 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 203) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/203 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/203' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C(=O)NCC(F)F) `ZINC001342965474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342965474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342965474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001342965474 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C(=O)NCC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 11, 8, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 15, 15, 15, 16, 16, 16, 49, 50, 50, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 16, 49, 49, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342965474 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001342965474 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342965474/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342965474/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342965474 Building ZINC001342965474 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342965474' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342965474 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342965474 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342965474/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342965474 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 202) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/202: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C(=O)NCC(F)F) `ZINC001342965474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342965474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342965474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001342965474 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C(=O)NCC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 11, 8, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 18, 18, 18, 48, 50, 50, 8, 8, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 18, 48, 48, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342965474 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342965474/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342965474 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 203) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/203: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C(=O)NCC(F)F) `ZINC001342965474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342965474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342965474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001342965474 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C(=O)NCC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 11, 8, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 15, 15, 15, 16, 16, 16, 49, 50, 50, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 16, 49, 49, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342965474 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001342965474 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342965474/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342965474/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342965474 Building ZINC001342966757 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342966757' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342966757 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342966757 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342966757/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342966757 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/204 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCCNC(N)=O) `ZINC001342966757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342966757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342966757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001342966757 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 6, 6, 20, 26, 28, 49, 50, 50, 50, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 20, 20, 28, 28, 28, 28, 49, 49, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342966757 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342966757/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342966757 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 205) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/205 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/205' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCCNC(N)=O) `ZINC001342966757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342966757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342966757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001342966757 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 6, 6, 24, 30, 34, 49, 50, 50, 50, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 24, 24, 34, 34, 34, 34, 49, 49, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342966757 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001342966757 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342966757/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342966757/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342966757 Building ZINC001342966757 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342966757' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342966757 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342966757 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342966757/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342966757 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 204) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/204: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCCNC(N)=O) `ZINC001342966757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342966757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342966757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001342966757 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 6, 6, 20, 26, 28, 49, 50, 50, 50, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 20, 20, 28, 28, 28, 28, 49, 49, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342966757 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342966757/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342966757 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 205) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/205: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCCNC(N)=O) `ZINC001342966757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342966757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342966757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001342966757 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCCCNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 6, 6, 24, 30, 34, 49, 50, 50, 50, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 24, 24, 34, 34, 34, 34, 49, 49, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342966757 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001342966757 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342966757/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342966757/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342966757 Building ZINC001342967617 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342967617' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342967617 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342967617 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342967617/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342967617 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/206 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCS(C)(=O)=O) `ZINC001342967617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342967617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342967617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001342967617 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 15, 15, 15, 36, 37, 50, 50, 50, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 36, 36, 37, 37, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342967617 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342967617/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342967617 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 207) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/207 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/207' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCS(C)(=O)=O) `ZINC001342967617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342967617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342967617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001342967617 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 7, 7, 7, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 18, 18, 18, 37, 39, 50, 50, 50, 11, 11, 11, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 18, 37, 37, 39, 39, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342967617 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001342967617 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342967617/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342967617/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342967617 Building ZINC001342967617 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342967617' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342967617 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001342967617 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342967617/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342967617 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 206) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/206: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCS(C)(=O)=O) `ZINC001342967617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001342967617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342967617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001342967617 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 15, 15, 15, 36, 37, 50, 50, 50, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 36, 36, 37, 37, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342967617 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342967617/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342967617 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 207) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/207: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCS(C)(=O)=O) `ZINC001342967617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001342967617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342967617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001342967617 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 7, 7, 7, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 18, 18, 18, 37, 39, 50, 50, 50, 11, 11, 11, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 18, 37, 37, 39, 39, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342967617 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001342967617 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342967617/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342967617/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001342967617 Building ZINC001343014007 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343014007' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343014007 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343014007 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343014007/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343014007 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/208 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CCC1) `ZINC001343014007.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343014007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343014007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343014007 none CNC(=O)C1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 50, 24, 14, 14, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 6, 40, 40, 40, 50, 50, 50, 50, 14, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 156 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343014007 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343014007/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343014007 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 209) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/209 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/209' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CCC1) `ZINC001343014007.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343014007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343014007/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343014007 none CNC(=O)C1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 50, 23, 12, 12, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 43, 43, 43, 50, 50, 50, 50, 12, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 154 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343014007 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343014007 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343014007/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343014007/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343014007 Building ZINC001343014007 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343014007' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343014007 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343014007 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343014007/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343014007 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 208) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/208: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CCC1) `ZINC001343014007.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343014007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343014007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343014007 none CNC(=O)C1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 50, 24, 14, 14, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 6, 40, 40, 40, 50, 50, 50, 50, 14, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 156 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343014007 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343014007/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343014007 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 209) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/209: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CCC1) `ZINC001343014007.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343014007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343014007/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343014007 none CNC(=O)C1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2OC)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 50, 23, 12, 12, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 43, 43, 43, 50, 50, 50, 50, 12, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 154 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343014007 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343014007 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343014007/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343014007/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343014007 Building ZINC001343060260 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343060260' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343060260 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343060260 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343060260/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343060260 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/210 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C(=O)NCC1CC1) `ZINC001343060260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343060260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343060260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001343060260 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 15, 15, 15, 17, 17, 17, 38, 50, 50, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 17, 38, 38, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343060260 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343060260/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343060260 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 211) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/211 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/211' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C(=O)NCC1CC1) `ZINC001343060260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343060260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343060260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001343060260 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 18, 18, 18, 19, 19, 19, 42, 50, 50, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 19, 42, 42, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343060260 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343060260 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343060260/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343060260/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343060260 Building ZINC001343060260 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343060260' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343060260 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343060260 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343060260/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343060260 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 210) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/210: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C(=O)NCC1CC1) `ZINC001343060260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343060260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343060260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001343060260 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 15, 15, 15, 17, 17, 17, 38, 50, 50, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 17, 38, 38, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343060260 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343060260/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343060260 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 211) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/211: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C(=O)NCC1CC1) `ZINC001343060260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343060260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343060260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001343060260 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)C(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 18, 18, 18, 19, 19, 19, 42, 50, 50, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 19, 42, 42, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343060260 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343060260 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343060260/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343060260/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343060260 Building ZINC001343268595 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268595' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268595 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268595 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268595/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268595 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/212 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343268595.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343268595 none C[C@@H]1CCCN(C(=O)C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 49, 20, 38, 13, 20, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268595 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268595/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268595 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 213) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/213 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/213' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343268595.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343268595 none C[C@@H]1CCCN(C(=O)C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 45, 19, 35, 11, 19, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 166 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268595 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343268595 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268595/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268595/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268595 Building ZINC001343268595 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268595' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268595 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268595 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268595/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268595 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 212) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/212: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343268595.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343268595 none C[C@@H]1CCCN(C(=O)C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 49, 20, 38, 13, 20, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268595 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268595/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268595 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 213) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/213: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343268595.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343268595 none C[C@@H]1CCCN(C(=O)C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 45, 19, 35, 11, 19, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 166 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268595 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343268595 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268595/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268595/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268595 Building ZINC001343268597 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268597' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268597 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268597 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268597/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268597 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/214 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343268597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343268597 none C[C@H]1CCCN(C(=O)C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 47, 19, 36, 13, 19, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268597 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268597/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268597 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 215) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/215 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/215' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343268597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343268597 none C[C@H]1CCCN(C(=O)C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 48, 17, 38, 11, 17, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 169 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268597 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343268597 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268597/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268597/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268597 Building ZINC001343268597 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268597' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268597 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268597 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268597/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268597 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 214) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/214: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343268597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343268597 none C[C@H]1CCCN(C(=O)C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 47, 19, 36, 13, 19, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268597 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268597/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268597 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 215) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/215: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343268597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343268597 none C[C@H]1CCCN(C(=O)C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 48, 17, 38, 11, 17, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 169 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268597 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343268597 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268597/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268597/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268597 Building ZINC001343268628 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268628' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268628 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268628 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268628/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268628 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/216 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3nn[nH]c32)C[C@@H]1O) `ZINC001343268628.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001343268628 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3nn[nH]c32)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 6, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 153 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268628 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268628/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268628 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 217) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/217 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/217' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3nn[nH]c32)C[C@@H]1O) `ZINC001343268628.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268628/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001343268628 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3nn[nH]c32)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 6, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268628 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343268628 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268628/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268628/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268628 Building ZINC001343268628 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268628' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268628 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268628 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268628/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268628 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 216) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/216: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3nn[nH]c32)C[C@@H]1O) `ZINC001343268628.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001343268628 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3nn[nH]c32)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 6, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 153 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268628 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268628/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268628 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 217) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/217: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3nn[nH]c32)C[C@@H]1O) `ZINC001343268628.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268628/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001343268628 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3nn[nH]c32)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 6, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268628 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343268628 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268628/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268628/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268628 Building ZINC001343268677 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268677' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268677 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268677 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268677/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268677 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/218 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1) `ZINC001343268677.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001343268677 none C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 17, 30, 11, 17, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 30, 50, 50, 50, 50, 50, 30, 30, 30, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 179 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268677 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268677/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268677 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 219) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/219 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/219' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1) `ZINC001343268677.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268677/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001343268677 none C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 19, 31, 8, 19, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 31, 50, 50, 50, 50, 50, 31, 31, 31, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268677 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343268677 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268677/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268677/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268677 Building ZINC001343268677 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268677' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268677 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268677 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268677/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268677 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 218) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/218: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1) `ZINC001343268677.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001343268677 none C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 17, 30, 11, 17, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 30, 50, 50, 50, 50, 50, 30, 30, 30, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 179 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268677 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268677/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268677 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 219) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/219: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1) `ZINC001343268677.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268677/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001343268677 none C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 19, 31, 8, 19, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 31, 50, 50, 50, 50, 50, 31, 31, 31, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268677 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343268677 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268677/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268677/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268677 Building ZINC001343268678 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268678' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268678 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268678 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268678/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268678 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/220 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1) `ZINC001343268678.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001343268678 none C[C@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 13, 29, 8, 13, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 29, 50, 50, 50, 50, 50, 29, 29, 29, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268678 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268678/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268678 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 221) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/221 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/221' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1) `ZINC001343268678.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268678/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001343268678 none C[C@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 16, 31, 7, 16, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 31, 50, 50, 50, 50, 50, 31, 31, 31, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 7, 7, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 164 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268678 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343268678 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268678/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268678/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268678 Building ZINC001343268678 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268678' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268678 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268678 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268678/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268678 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 220) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/220: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1) `ZINC001343268678.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001343268678 none C[C@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 13, 29, 8, 13, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 29, 50, 50, 50, 50, 50, 29, 29, 29, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268678 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268678/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268678 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 221) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/221: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1) `ZINC001343268678.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268678/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001343268678 none C[C@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 16, 31, 7, 16, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 31, 50, 50, 50, 50, 50, 31, 31, 31, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 7, 7, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 164 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268678 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343268678 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268678/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268678/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268678 Building ZINC001343268856 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268856' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268856 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268856 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268856/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268856 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/222 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cnc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001343268856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343268856 none CC(C)(C)n1cnc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 17, 8, 17, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 119 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268856 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268856/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268856 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 223) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/223 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/223' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cnc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001343268856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343268856 none CC(C)(C)n1cnc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 17, 10, 17, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268856 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343268856 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268856/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268856/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268856 Building ZINC001343268856 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268856' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268856 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343268856 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268856/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268856 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 222) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/222: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cnc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001343268856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343268856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343268856 none CC(C)(C)n1cnc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 17, 8, 17, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 119 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268856 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268856/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268856 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 223) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/223: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cnc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001343268856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343268856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001343268856 none CC(C)(C)n1cnc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 17, 10, 17, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268856 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343268856 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268856/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268856/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343268856 Building ZINC001343269113 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269113' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269113 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269113 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269113/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269113 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/224 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cnn1C) `ZINC001343269113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001343269113 none CCc1c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 38, 38, 24, 11, 24, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 38, 38, 38, 38, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 38, 38, 38, 38] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269113 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269113/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269113 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 225) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/225 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/225' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cnn1C) `ZINC001343269113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001343269113 none CCc1c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 36, 36, 23, 10, 23, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 36, 36, 36, 36, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 36, 36, 36, 36] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 209 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269113 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343269113 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269113/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269113/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269113 Building ZINC001343269113 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269113' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269113 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269113 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269113/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269113 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 224) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/224: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cnn1C) `ZINC001343269113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001343269113 none CCc1c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 38, 38, 24, 11, 24, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 38, 38, 38, 38, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 38, 38, 38, 38] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269113 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269113/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269113 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 225) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/225: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cnn1C) `ZINC001343269113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001343269113 none CCc1c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 36, 36, 23, 10, 23, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 36, 36, 36, 36, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 36, 36, 36, 36] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 209 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269113 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343269113 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269113/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269113/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269113 Building ZINC001343269502 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269502' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269502 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269502 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269502/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269502 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/226 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCO[C@H](C)C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343269502 none CCOCCO[C@H](C)C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 49, 40, 22, 12, 5, 12, 12, 5, 5, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 49, 49, 40, 40, 12, 12, 12, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5] 150 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269502 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269502/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269502 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 227) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/227 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/227' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCO[C@H](C)C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343269502 none CCOCCO[C@H](C)C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 49, 43, 27, 19, 6, 19, 19, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 50, 49, 49, 43, 43, 19, 19, 19, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6] 150 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 217 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269502 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343269502 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269502/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269502/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269502 Building ZINC001343269502 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269502' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269502 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269502 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269502/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269502 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 226) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/226: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCO[C@H](C)C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343269502 none CCOCCO[C@H](C)C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 49, 40, 22, 12, 5, 12, 12, 5, 5, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 49, 49, 40, 40, 12, 12, 12, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5] 150 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269502 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269502/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269502 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 227) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/227: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCO[C@H](C)C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343269502 none CCOCCO[C@H](C)C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 49, 43, 27, 19, 6, 19, 19, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 50, 49, 49, 43, 43, 19, 19, 19, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6] 150 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 217 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269502 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343269502 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269502/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269502/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269502 Building ZINC001343269503 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269503' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269503 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269503 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269503/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269503 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/228 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCO[C@@H](C)C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343269503 none CCOCCO[C@@H](C)C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 46, 37, 22, 16, 5, 16, 16, 4, 5, 4, 4, 2, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 46, 46, 37, 37, 16, 16, 16, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 4, 4] 150 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269503 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269503/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269503 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 229) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/229 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/229' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCO[C@@H](C)C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343269503 none CCOCCO[C@@H](C)C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 45, 29, 19, 6, 19, 19, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 45, 45, 19, 19, 19, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6] 150 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 221 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269503 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343269503 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269503/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269503/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269503 Building ZINC001343269503 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269503' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269503 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269503 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269503/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269503 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 228) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/228: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCO[C@@H](C)C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343269503 none CCOCCO[C@@H](C)C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 46, 37, 22, 16, 5, 16, 16, 4, 5, 4, 4, 2, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 46, 46, 37, 37, 16, 16, 16, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 4, 4] 150 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269503 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269503/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269503 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 229) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/229: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCO[C@@H](C)C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343269503 none CCOCCO[C@@H](C)C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 45, 29, 19, 6, 19, 19, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 45, 45, 19, 19, 19, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6] 150 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 221 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269503 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343269503 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269503/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269503/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269503 Building ZINC001343269595 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269595' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269595 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269595 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269595/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269595 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/230 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccnc1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269595.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001343269595 none COc1cccnc1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 26, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 26, 26, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 7, 7] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 153 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269595 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269595/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269595 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 231) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/231 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/231' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccnc1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269595.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001343269595 none COc1cccnc1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 27, 5, 5, 5, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 27, 27, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269595 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343269595 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269595/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269595/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269595 Building ZINC001343269595 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269595' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269595 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269595 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269595/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269595 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 230) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/230: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccnc1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269595.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001343269595 none COc1cccnc1CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 26, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 26, 26, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 7, 7] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 153 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269595 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269595/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269595 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 231) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/231: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccnc1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343269595.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001343269595 none COc1cccnc1CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 27, 5, 5, 5, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 27, 27, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269595 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343269595 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269595/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269595/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269595 Building ZINC001343269615 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269615' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269615 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269615 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269615/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269615 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/232 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CCC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1) `ZINC001343269615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001343269615 none Cn1cc(CCC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 33, 31, 10, 8, 10, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 33, 33, 31, 31, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 183 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269615 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269615/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269615 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 233) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/233 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/233' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CCC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1) `ZINC001343269615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001343269615 none Cn1cc(CCC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 39, 34, 13, 9, 13, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 39, 39, 34, 34, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269615 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343269615 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269615/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269615/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269615 Building ZINC001343269615 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269615' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269615 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269615 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269615/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269615 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 232) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/232: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CCC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1) `ZINC001343269615.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001343269615 none Cn1cc(CCC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 33, 31, 10, 8, 10, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 33, 33, 31, 31, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 183 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269615 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269615/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269615 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 233) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/233: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CCC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1) `ZINC001343269615.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001343269615 none Cn1cc(CCC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 39, 34, 13, 9, 13, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 39, 39, 34, 34, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269615 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343269615 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269615/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269615/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269615 Building ZINC001343269641 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269641' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269641 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269641 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269641/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269641 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/234 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cn2cc(Cl)cn2)C[C@@H]1O) `ZINC001343269641.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001343269641 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cn2cc(Cl)cn2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 16, 1, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 9, 9, 33, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 33, 33, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 171 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269641 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269641/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269641 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 235) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/235 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/235' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cn2cc(Cl)cn2)C[C@@H]1O) `ZINC001343269641.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269641/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001343269641 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cn2cc(Cl)cn2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 16, 1, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 10, 10, 32, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 32, 32, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269641 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343269641 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269641/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269641/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269641 Building ZINC001343269641 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269641' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269641 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343269641 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269641/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269641 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 234) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/234: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cn2cc(Cl)cn2)C[C@@H]1O) `ZINC001343269641.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343269641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001343269641 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cn2cc(Cl)cn2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 16, 1, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 9, 9, 33, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 33, 33, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 171 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269641 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269641/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269641 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 235) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/235: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cn2cc(Cl)cn2)C[C@@H]1O) `ZINC001343269641.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343269641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269641/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001343269641 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)Cn2cc(Cl)cn2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 16, 1, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 10, 10, 32, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 32, 32, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269641 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343269641 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269641/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269641/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343269641 Building ZINC001343270141 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270141' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270141 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270141/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/236 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2CCN(C(N)=O)CC2)C[C@@H]1O) `ZINC001343270141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270141 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2CCN(C(N)=O)CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 8, 11, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 11, 20, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 168 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270141/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 237) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/237 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/237' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2CCN(C(N)=O)CC2)C[C@@H]1O) `ZINC001343270141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270141 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2CCN(C(N)=O)CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 8, 11, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 13, 27, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 162 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343270141 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270141/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270141/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270141 Building ZINC001343270141 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270141' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270141 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270141/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 236) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/236: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2CCN(C(N)=O)CC2)C[C@@H]1O) `ZINC001343270141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270141 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2CCN(C(N)=O)CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 8, 11, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 11, 20, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 168 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270141/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 237) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/237: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2CCN(C(N)=O)CC2)C[C@@H]1O) `ZINC001343270141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270141 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C2CCN(C(N)=O)CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 8, 11, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 13, 27, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 162 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343270141 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270141/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270141/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270141 Building ZINC001343270235 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270235 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/238 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270235 none CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 20, 50, 11, 20, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 174 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 239) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/239 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/239' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270235 none CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 20, 50, 11, 20, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 174 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 240) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/240 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/240' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270235.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270235 none CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 22, 50, 13, 22, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 174 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 241) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/241 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/241' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270235.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270235 none CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 22, 50, 13, 22, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 174 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343270235 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 Building ZINC001343270235 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270235 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 238) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/238: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270235 none CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 20, 50, 11, 20, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 174 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 239) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/239: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270235 none CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 20, 50, 11, 20, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 174 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 240) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270235.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270235 none CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 22, 50, 13, 22, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 174 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 241) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270235.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270235 none CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 22, 50, 13, 22, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 174 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343270235 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 Building ZINC001343270235 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270235 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 238) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/238: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270235 none CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 20, 50, 11, 20, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 174 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 239) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/239: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270235 none CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 20, 50, 11, 20, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 174 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 240) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270235.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270235 none CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 22, 50, 13, 22, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 174 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 241) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270235.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270235 none CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 22, 50, 13, 22, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 174 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343270235 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 Building ZINC001343270235 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270235 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 238) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/238: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270235 none CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 20, 50, 11, 20, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 174 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 239) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/239: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270235 none CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 20, 50, 11, 20, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 174 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 240) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270235.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270235 none CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 22, 50, 13, 22, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 174 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 241) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270235.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270235 none CCN1CCO[C@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 22, 50, 13, 22, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 174 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343270235 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270235 Building ZINC001343270238 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270238 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/242 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270238 none CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 24, 50, 13, 24, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 243) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/243 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/243' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270238 none CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 24, 50, 13, 24, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 244) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/244 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/244' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270238.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270238 none CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 50, 13, 25, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 245) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/245 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/245' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270238.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270238 none CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 50, 13, 25, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343270238 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 Building ZINC001343270238 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270238 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 242) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/242: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270238 none CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 24, 50, 13, 24, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 243) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/243: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270238 none CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 24, 50, 13, 24, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 244) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/244: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270238.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270238 none CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 50, 13, 25, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 245) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/245: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270238.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270238 none CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 50, 13, 25, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343270238 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 Building ZINC001343270238 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270238 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 242) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/242: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270238 none CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 24, 50, 13, 24, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 243) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/243: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270238 none CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 24, 50, 13, 24, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 244) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/244: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270238.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270238 none CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 50, 13, 25, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 245) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/245: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270238.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270238 none CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 50, 13, 25, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343270238 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 Building ZINC001343270238 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270238 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 242) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/242: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270238 none CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 24, 50, 13, 24, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 243) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/243: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270238 none CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 24, 50, 13, 24, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 244) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/244: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270238.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270238 none CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 50, 13, 25, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 245) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/245: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1) `ZINC001343270238.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270238 none CCN1CCO[C@@H](C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 50, 13, 25, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343270238 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270238 Building ZINC001343270256 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270256' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270256 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270256 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270256/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270256 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/246 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COCc2cccnc2)C[C@@H]1O) `ZINC001343270256.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001343270256 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COCc2cccnc2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 15, 25, 35, 50, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 35, 35, 50, 50, 50, 50, 5, 5, 15] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 161 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270256 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270256/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270256 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 247) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/247 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/247' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COCc2cccnc2)C[C@@H]1O) `ZINC001343270256.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270256/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001343270256 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COCc2cccnc2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 12, 22, 33, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 12, 12, 33, 33, 50, 50, 50, 50, 2, 2, 6] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270256 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343270256 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270256/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270256/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270256 Building ZINC001343270256 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270256' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270256 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270256 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270256/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270256 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 246) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/246: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COCc2cccnc2)C[C@@H]1O) `ZINC001343270256.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001343270256 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COCc2cccnc2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 15, 25, 35, 50, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 35, 35, 50, 50, 50, 50, 5, 5, 15] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 161 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270256 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270256/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270256 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 247) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/247: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COCc2cccnc2)C[C@@H]1O) `ZINC001343270256.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270256/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001343270256 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COCc2cccnc2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 12, 22, 33, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 12, 12, 33, 33, 50, 50, 50, 50, 2, 2, 6] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270256 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343270256 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270256/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270256/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270256 Building ZINC001343270377 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270377' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270377 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270377 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270377/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270377 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/248 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(CCC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1) `ZINC001343270377.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001343270377 none Cc1cnn(CCC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 34, 28, 9, 8, 9, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 34, 34, 28, 28, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270377 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270377/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270377 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 249) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/249 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/249' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(CCC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1) `ZINC001343270377.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270377/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001343270377 none Cc1cnn(CCC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 32, 29, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 32, 32, 29, 29, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270377 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343270377 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270377/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270377/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270377 Building ZINC001343270377 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270377' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270377 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270377 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270377/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270377 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 248) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/248: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(CCC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1) `ZINC001343270377.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001343270377 none Cc1cnn(CCC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 34, 28, 9, 8, 9, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 34, 34, 28, 28, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270377 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270377/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270377 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 249) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/249: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(CCC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1) `ZINC001343270377.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270377/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001343270377 none Cc1cnn(CCC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 32, 29, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 32, 32, 29, 29, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270377 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343270377 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270377/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270377/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270377 Building ZINC001343270899 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270899' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270899 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270899 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270899/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270899 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/250 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(Cl)ncc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270899.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001343270899 none Cn1c(Cl)ncc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'Cl', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 16, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 35, 12, 35, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44]) total number of confs: 159 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270899 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270899/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270899 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 251) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/251 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/251' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(Cl)ncc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270899.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001343270899 none Cn1c(Cl)ncc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'Cl', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 16, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 30, 14, 30, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270899 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343270899 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270899/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270899/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270899 Building ZINC001343270899 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270899' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270899 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270899 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270899/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270899 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 250) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/250: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(Cl)ncc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270899.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001343270899 none Cn1c(Cl)ncc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'Cl', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 16, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 35, 12, 35, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44]) total number of confs: 159 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270899 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270899/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270899 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 251) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/251: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(Cl)ncc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270899.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001343270899 none Cn1c(Cl)ncc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'Cl', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 16, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 30, 14, 30, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270899 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343270899 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270899/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270899/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270899 Building ZINC001343270933 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270933 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/252 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270933 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 28, 50, 14, 28, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 193 number of broken/clashed sets: 129 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 253) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/253 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/253' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270933 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 28, 50, 14, 28, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 193 number of broken/clashed sets: 129 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 254) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/254 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/254' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270933.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270933 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 28, 50, 14, 28, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 191 number of broken/clashed sets: 128 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 255) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/255 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/255' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270933.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270933 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 28, 50, 14, 28, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 191 number of broken/clashed sets: 128 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343270933 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 Building ZINC001343270933 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270933 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 252) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/252: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270933 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 28, 50, 14, 28, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 193 number of broken/clashed sets: 129 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 253) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/253: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270933 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 28, 50, 14, 28, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 193 number of broken/clashed sets: 129 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 254) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/254: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270933.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270933 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 28, 50, 14, 28, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 191 number of broken/clashed sets: 128 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 255) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/255: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270933.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270933 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 28, 50, 14, 28, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 191 number of broken/clashed sets: 128 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343270933 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 Building ZINC001343270933 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270933 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 252) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/252: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270933 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 28, 50, 14, 28, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 193 number of broken/clashed sets: 129 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 253) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/253: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270933 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 28, 50, 14, 28, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 193 number of broken/clashed sets: 129 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 254) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/254: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270933.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270933 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 28, 50, 14, 28, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 191 number of broken/clashed sets: 128 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 255) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/255: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270933.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270933 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 28, 50, 14, 28, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 191 number of broken/clashed sets: 128 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343270933 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 Building ZINC001343270933 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270933 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 252) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/252: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270933 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 28, 50, 14, 28, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 193 number of broken/clashed sets: 129 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 253) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/253: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270933 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 28, 50, 14, 28, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 193 number of broken/clashed sets: 129 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 254) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/254: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270933.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270933 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 28, 50, 14, 28, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 191 number of broken/clashed sets: 128 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 255) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/255: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270933.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270933 none CCN1CCOC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 28, 50, 14, 28, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 191 number of broken/clashed sets: 128 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343270933 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270933 Building ZINC001343270936 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270936 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/256 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270936 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 30, 50, 13, 30, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 188 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 257) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/257 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/257' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270936 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 30, 50, 13, 30, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 188 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 258) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/258 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/258' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270936.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270936 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 50, 14, 32, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 189 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 259) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/259 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/259' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270936.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270936 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 50, 14, 32, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 189 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343270936 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 Building ZINC001343270936 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270936 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 256) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/256: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270936 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 30, 50, 13, 30, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 188 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 257) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/257: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270936 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 30, 50, 13, 30, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 188 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 258) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/258: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270936.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270936 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 50, 14, 32, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 189 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 259) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/259: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270936.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270936 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 50, 14, 32, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 189 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343270936 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 Building ZINC001343270936 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270936 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 256) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/256: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270936 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 30, 50, 13, 30, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 188 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 257) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/257: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270936 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 30, 50, 13, 30, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 188 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 258) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/258: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270936.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270936 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 50, 14, 32, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 189 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 259) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/259: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270936.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270936 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 50, 14, 32, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 189 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343270936 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 Building ZINC001343270936 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001343270936 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 256) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/256: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270936 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 30, 50, 13, 30, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 188 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 257) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/257: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270936 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 30, 50, 13, 30, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 188 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 258) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/258: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270936.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001343270936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270936 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 50, 14, 32, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 189 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 259) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/259: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343270936.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001343270936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343270936 none CCN1CCOC[C@@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 50, 14, 32, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 189 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343270936 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270936 Building ZINC001343270952 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270952' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270952 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270952 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270952/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270952 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/260 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(CCC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001343270952.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001343270952 none Cn1ncc(CCC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 34, 31, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 50, 50, 50, 50, 50, 34, 34, 31, 31, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 7, 7] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 172 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270952 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270952/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270952 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 261) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/261 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/261' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(CCC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001343270952.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001343270952 none Cn1ncc(CCC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 34, 29, 9, 7, 9, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 50, 50, 50, 50, 50, 34, 34, 29, 29, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 7, 7] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270952 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343270952 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270952/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270952/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270952 Building ZINC001343270952 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270952' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270952 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343270952 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270952/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270952 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 260) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/260: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(CCC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001343270952.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343270952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001343270952 none Cn1ncc(CCC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 34, 31, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 50, 50, 50, 50, 50, 34, 34, 31, 31, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 7, 7] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 172 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270952 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270952/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270952 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 261) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/261: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(CCC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001343270952.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343270952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001343270952 none Cn1ncc(CCC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 34, 29, 9, 7, 9, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 50, 50, 50, 50, 50, 34, 34, 29, 29, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 7, 7] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270952 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343270952 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270952/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270952/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343270952 Building ZINC001343271373 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271373' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271373 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343271373 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271373/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271373 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/262 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)NCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343271373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343271373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343271373 none CC(C)(C)C(=O)NCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 40, 15, 9, 15, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271373 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271373/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271373 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 263) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/263 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/263' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)NCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343271373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343271373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343271373 none CC(C)(C)C(=O)NCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 37, 15, 10, 15, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 209 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271373 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343271373 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271373/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271373/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271373 Building ZINC001343271373 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271373' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271373 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343271373 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271373/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271373 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 262) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/262: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)NCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343271373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343271373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343271373 none CC(C)(C)C(=O)NCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 40, 15, 9, 15, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271373 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271373/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271373 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 263) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/263: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)NCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001343271373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343271373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343271373 none CC(C)(C)C(=O)NCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 37, 15, 10, 15, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 37, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 209 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271373 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343271373 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271373/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271373/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271373 Building ZINC001343271607 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271607' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271607 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343271607 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271607/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271607 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/264 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc[nH]c3nccc2-3)C[C@@H]1O) `ZINC001343271607.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343271607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001343271607 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc[nH]c3nccc2-3)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 1, 8, 6, 1, 8, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 161 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271607 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271607/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271607 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 265) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/265 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/265' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc[nH]c3nccc2-3)C[C@@H]1O) `ZINC001343271607.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343271607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001343271607 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc[nH]c3nccc2-3)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 1, 8, 6, 1, 8, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271607 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343271607 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271607/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271607/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271607 Building ZINC001343271607 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271607' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271607 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343271607 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271607/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271607 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 264) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/264: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc[nH]c3nccc2-3)C[C@@H]1O) `ZINC001343271607.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343271607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001343271607 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc[nH]c3nccc2-3)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 1, 8, 6, 1, 8, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 161 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271607 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271607/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271607 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 265) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/265: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc[nH]c3nccc2-3)C[C@@H]1O) `ZINC001343271607.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343271607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001343271607 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc[nH]c3nccc2-3)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 1, 8, 6, 1, 8, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271607 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343271607 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271607/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271607/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271607 Building ZINC001343271895 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271895' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271895 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343271895 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271895/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271895 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/266 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCCC1) `ZINC001343271895.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343271895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343271895 none CC(=O)NC1(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 33, 25, 15, 25, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 33, 33, 33, 33, 50, 50, 50, 50, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15, 33, 33, 33, 33, 33, 33, 33, 33] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 218 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271895 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271895/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271895 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 267) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/267 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/267' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCCC1) `ZINC001343271895.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343271895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271895/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343271895 none CC(=O)NC1(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 38, 28, 17, 28, 17, 17, 3, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 38, 38, 38, 38, 50, 50, 50, 50, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 17, 17, 38, 38, 38, 38, 38, 38, 38, 38] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 220 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271895 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343271895 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271895/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271895/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271895 Building ZINC001343271895 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271895' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271895 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343271895 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271895/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271895 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 266) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/266: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCCC1) `ZINC001343271895.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343271895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343271895 none CC(=O)NC1(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 33, 25, 15, 25, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 33, 33, 33, 33, 50, 50, 50, 50, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 15, 15, 33, 33, 33, 33, 33, 33, 33, 33] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 218 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271895 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271895/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271895 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 267) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/267: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCCC1) `ZINC001343271895.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343271895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271895/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343271895 none CC(=O)NC1(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 38, 28, 17, 28, 17, 17, 3, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 38, 38, 38, 38, 50, 50, 50, 50, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 17, 17, 38, 38, 38, 38, 38, 38, 38, 38] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 220 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271895 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343271895 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271895/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271895/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343271895 Building ZINC001343436747 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436747' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436747 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343436747 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436747/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436747 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/268 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C[C@@H](F)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343436747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343436747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343436747 none CCN(CC)C[C@@H](F)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 43, 35, 43, 50, 30, 11, 30, 30, 11, 11, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 263 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436747 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436747/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436747 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 269) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/269 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/269' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C[C@@H](F)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343436747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343436747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343436747 none CCN(CC)C[C@@H](F)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 40, 28, 40, 50, 21, 9, 21, 21, 9, 9, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 292 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436747 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343436747 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436747/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436747/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436747 Building ZINC001343436747 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436747' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436747 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343436747 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436747/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436747 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 268) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/268: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C[C@@H](F)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343436747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343436747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343436747 none CCN(CC)C[C@@H](F)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 43, 35, 43, 50, 30, 11, 30, 30, 11, 11, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 263 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436747 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436747/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436747 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 269) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/269: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C[C@@H](F)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343436747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343436747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343436747 none CCN(CC)C[C@@H](F)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 40, 28, 40, 50, 21, 9, 21, 21, 9, 9, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 292 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436747 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343436747 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436747/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436747/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436747 Building ZINC001343436749 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436749' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436749 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343436749 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436749/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436749 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/270 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C[C@H](F)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343436749.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343436749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343436749 none CCN(CC)C[C@H](F)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 42, 39, 42, 50, 30, 14, 30, 30, 14, 14, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 277 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436749 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436749/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436749 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 271) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/271 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/271' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C[C@H](F)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343436749.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343436749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436749/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343436749 none CCN(CC)C[C@H](F)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 40, 30, 40, 50, 21, 9, 21, 21, 9, 9, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 9, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9] 150 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 295 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436749 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343436749 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436749/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436749/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436749 Building ZINC001343436749 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436749' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436749 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343436749 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436749/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436749 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 270) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/270: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C[C@H](F)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343436749.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343436749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343436749 none CCN(CC)C[C@H](F)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 42, 39, 42, 50, 30, 14, 30, 30, 14, 14, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 277 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436749 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436749/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436749 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 271) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/271: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C[C@H](F)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343436749.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343436749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436749/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001343436749 none CCN(CC)C[C@H](F)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 7, 15, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 40, 30, 40, 50, 21, 9, 21, 21, 9, 9, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 9, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9] 150 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 295 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436749 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343436749 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436749/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436749/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343436749 Building ZINC001343449616 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343449616' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343449616 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343449616 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343449616/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343449616 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/272 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O)C(=O)C1CC1) `ZINC001343449616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343449616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343449616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343449616 none CN(CC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 16, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 37, 37, 50, 50, 27, 27, 27, 16, 16, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50] 150 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 46, 47, 48, 49, 50, 51]) total number of confs: 188 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343449616 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343449616/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343449616 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 273) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/273 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/273' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O)C(=O)C1CC1) `ZINC001343449616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343449616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343449616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343449616 none CN(CC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 19, 5, 5, 5, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 27, 35, 35, 50, 50, 27, 27, 27, 19, 19, 5, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 9, 10, 43, 12, 13, 14, 15, 16, 17, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 190 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343449616 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343449616 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343449616/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343449616/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343449616 Building ZINC001343449616 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343449616' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343449616 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343449616 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343449616/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343449616 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 272) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/272: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O)C(=O)C1CC1) `ZINC001343449616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343449616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343449616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343449616 none CN(CC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 16, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 37, 37, 50, 50, 27, 27, 27, 16, 16, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50] 150 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 46, 47, 48, 49, 50, 51]) total number of confs: 188 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343449616 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343449616/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343449616 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 273) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/273: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O)C(=O)C1CC1) `ZINC001343449616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343449616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343449616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001343449616 none CN(CC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 19, 5, 5, 5, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 27, 35, 35, 50, 50, 27, 27, 27, 19, 19, 5, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 9, 10, 43, 12, 13, 14, 15, 16, 17, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 190 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343449616 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343449616 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343449616/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343449616/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343449616 Building ZINC001343534573 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343534573' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343534573 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343534573 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343534573/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343534573 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/274 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(C)(C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343534573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343534573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343534573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343534573 none CC(=O)NCC(C)(C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 48, 35, 17, 35, 35, 17, 17, 8, 8, 8, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 48, 48, 35, 35, 35, 35, 35, 35, 17, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 24] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343534573 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343534573/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343534573 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 275) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/275 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/275' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(C)(C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343534573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343534573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343534573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343534573 none CC(=O)NCC(C)(C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 45, 30, 12, 30, 30, 12, 12, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 45, 45, 30, 30, 30, 30, 30, 30, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343534573 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343534573 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343534573/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343534573/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343534573 Building ZINC001343534573 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343534573' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343534573 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343534573 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343534573/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343534573 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 274) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/274: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(C)(C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343534573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343534573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343534573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343534573 none CC(=O)NCC(C)(C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 48, 35, 17, 35, 35, 17, 17, 8, 8, 8, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 48, 48, 35, 35, 35, 35, 35, 35, 17, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 24] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343534573 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343534573/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343534573 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 275) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/275: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(C)(C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343534573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343534573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343534573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343534573 none CC(=O)NCC(C)(C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 45, 30, 12, 30, 30, 12, 12, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 45, 45, 30, 30, 30, 30, 30, 30, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343534573 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343534573 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343534573/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343534573/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343534573 Building ZINC001343577734 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343577734' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343577734 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343577734 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343577734/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343577734 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/276 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343577734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343577734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343577734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343577734 none CN(C)C(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 36, 38, 12, 12, 12, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 48, 50, 46, 46, 38, 38, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 276 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343577734 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343577734/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343577734 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 277) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/277 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/277' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343577734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343577734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343577734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343577734 none CN(C)C(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 33, 37, 13, 13, 13, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 46, 48, 43, 43, 37, 37, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 268 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343577734 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343577734 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343577734/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343577734/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343577734 Building ZINC001343577734 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343577734' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343577734 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343577734 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343577734/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343577734 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 276) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/276: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343577734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343577734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343577734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343577734 none CN(C)C(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 36, 38, 12, 12, 12, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 48, 50, 46, 46, 38, 38, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 276 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343577734 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343577734/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343577734 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 277) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/277: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343577734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343577734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343577734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343577734 none CN(C)C(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 33, 37, 13, 13, 13, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 46, 48, 43, 43, 37, 37, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 268 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343577734 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343577734 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343577734/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343577734/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343577734 Building ZINC001343766540 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343766540' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343766540 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343766540 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343766540/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343766540 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/278 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1CCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343766540.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343766540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343766540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343766540 none Cc1nn(C)cc1CCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 36, 34, 11, 11, 11, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 36, 36, 34, 34, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343766540 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343766540/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343766540 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 279) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/279 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/279' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1CCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343766540.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343766540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343766540/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343766540 none Cc1nn(C)cc1CCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 37, 35, 10, 10, 10, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 37, 37, 35, 35, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343766540 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343766540 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343766540/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343766540/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343766540 Building ZINC001343766540 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343766540' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343766540 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001343766540 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343766540/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343766540 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 278) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/278: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1CCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343766540.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001343766540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343766540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343766540 none Cc1nn(C)cc1CCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 36, 34, 11, 11, 11, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 36, 36, 34, 34, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343766540 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343766540/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343766540 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 279) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/279: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1CCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001343766540.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001343766540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343766540/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001343766540 none Cc1nn(C)cc1CCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 37, 35, 10, 10, 10, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 37, 37, 35, 35, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343766540 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001343766540 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343766540/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343766540/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001343766540 Building ZINC001344061095 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061095' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061095 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001344061095 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061095/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061095 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/280 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/280' -> `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]1CCCC[C@H]1NC(=O)[C@@H]1CC(=O)NC(=O)N1) `ZINC001344061095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001344061095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001344061095 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@@H]1CC(=O)NC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 1, 11, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 9, 9, 9, 17, 17, 28, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 9, 9, 17, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 145 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061095 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061095/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061095 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 281) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/281 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/281' -> `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]1CCCC[C@H]1NC(=O)[C@@H]1CC(=O)NC(=O)N1) `ZINC001344061095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001344061095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001344061095 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@@H]1CC(=O)NC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 1, 11, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 9, 9, 9, 17, 17, 22, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 9, 9, 17, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 143 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061095 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001344061095 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061095/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061095/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061095 Building ZINC001344061095 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061095' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061095 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001344061095 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061095/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061095 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 280) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/280: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@@H]1CC(=O)NC(=O)N1) `ZINC001344061095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001344061095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001344061095 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@@H]1CC(=O)NC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 1, 11, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 9, 9, 9, 17, 17, 28, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 9, 9, 17, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 145 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061095 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061095/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061095 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 281) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/281: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@@H]1CC(=O)NC(=O)N1) `ZINC001344061095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001344061095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001344061095 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)[C@@H]1CC(=O)NC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 1, 11, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 9, 9, 9, 17, 17, 22, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 9, 9, 17, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 143 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061095 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001344061095 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061095/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061095/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061095 Building ZINC001344061157 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061157' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061157 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001344061157 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061157/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061157 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/282 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/282' -> `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]1CCCC[C@H]1NC(=O)CN1C(=O)CNC1=O) `ZINC001344061157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001344061157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001344061157 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CN1C(=O)CNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 11, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 3, 10, 10, 10, 10, 10, 10, 10, 10, 14, 14, 14, 31, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 10, 10, 10, 10, 14, 31, 31, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061157 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061157/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061157 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 283) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/283 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/283' -> `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]1CCCC[C@H]1NC(=O)CN1C(=O)CNC1=O) `ZINC001344061157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001344061157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001344061157 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CN1C(=O)CNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 11, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 3, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 14, 37, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 8, 8, 14, 37, 37, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061157 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001344061157 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061157/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061157/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061157 Building ZINC001344061157 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061157' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061157 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001344061157 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061157/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061157 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 282) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/282: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CN1C(=O)CNC1=O) `ZINC001344061157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001344061157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001344061157 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CN1C(=O)CNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 11, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 3, 10, 10, 10, 10, 10, 10, 10, 10, 14, 14, 14, 31, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 10, 10, 10, 10, 14, 31, 31, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061157 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061157/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061157 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 283) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/283: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CN1C(=O)CNC1=O) `ZINC001344061157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001344061157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001344061157 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)CN1C(=O)CNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 11, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 3, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 14, 37, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 8, 8, 14, 37, 37, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061157 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001344061157 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061157/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061157/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344061157 Building ZINC001344147945 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147945' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147945 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001344147945 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147945/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147945 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/284 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001344147945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001344147945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001344147945 none CN(C[C@H]1CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 6, 11, 11, 11, 11, 11, 19, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147945 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147945/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147945 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 285) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/285 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/285' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001344147945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001344147945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001344147945 none CN(C[C@H]1CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 7, 12, 12, 12, 12, 12, 19, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147945 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001344147945 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147945/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147945/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147945 Building ZINC001344147945 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147945' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147945 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001344147945 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147945/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147945 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 284) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/284: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001344147945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001344147945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001344147945 none CN(C[C@H]1CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 6, 11, 11, 11, 11, 11, 19, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147945 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147945/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147945 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 285) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/285: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001344147945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001344147945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001344147945 none CN(C[C@H]1CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 7, 12, 12, 12, 12, 12, 19, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147945 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001344147945 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147945/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147945/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147945 Building ZINC001344147946 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147946' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147946 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001344147946 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147946/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147946 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/286 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001344147946.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001344147946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001344147946 none CN(C[C@@H]1CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 7, 10, 10, 10, 10, 10, 17, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147946 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147946/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147946 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 287) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/287 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/287' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001344147946.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001344147946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147946/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001344147946 none CN(C[C@@H]1CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 6, 10, 10, 10, 10, 10, 18, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147946 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001344147946 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147946/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147946/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147946 Building ZINC001344147946 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147946' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147946 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001344147946 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147946/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147946 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 286) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/286: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001344147946.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001344147946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001344147946 none CN(C[C@@H]1CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 7, 10, 10, 10, 10, 10, 17, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147946 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147946/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147946 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 287) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/287: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001344147946.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001344147946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147946/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001344147946 none CN(C[C@@H]1CCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 6, 10, 10, 10, 10, 10, 18, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147946 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001344147946 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147946/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147946/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344147946 Building ZINC001344379313 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344379313' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344379313 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001344379313 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344379313/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344379313 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/288 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1cncn1) `ZINC001344379313.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001344379313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344379313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001344379313 none CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 8, 22, 22, 22, 45, 50, 50, 50, 50, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 8, 22, 45, 45, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344379313 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344379313/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344379313 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 289) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/289 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/289' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1cncn1) `ZINC001344379313.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001344379313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344379313/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001344379313 none CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 20, 20, 20, 43, 50, 50, 50, 50, 6, 6, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 11, 20, 43, 43, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344379313 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001344379313 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344379313/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344379313/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344379313 Building ZINC001344379313 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344379313' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344379313 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001344379313 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344379313/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344379313 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 288) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/288: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1cncn1) `ZINC001344379313.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001344379313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344379313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001344379313 none CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 8, 22, 22, 22, 45, 50, 50, 50, 50, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 8, 22, 45, 45, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344379313 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344379313/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344379313 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 289) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/289: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1cncn1) `ZINC001344379313.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001344379313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344379313/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001344379313 none CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 20, 20, 20, 43, 50, 50, 50, 50, 6, 6, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 11, 20, 43, 43, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344379313 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001344379313 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344379313/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344379313/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344379313 Building ZINC001344395916 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344395916' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344395916 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001344395916 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344395916/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344395916 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/290 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)CCNC(N)=O)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001344395916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001344395916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344395916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001344395916 none CCO[C@@H]1CN(C(=O)CCNC(N)=O)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 16, 16, 16, 16, 16, 16, 18, 18, 30, 39, 50, 50, 50, 16, 10, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 16, 16, 30, 30, 39, 39, 50, 50, 50, 16, 16, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 55, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344395916 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344395916/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344395916 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 291) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/291 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/291' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)CCNC(N)=O)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001344395916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001344395916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344395916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001344395916 none CCO[C@@H]1CN(C(=O)CCNC(N)=O)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 13, 13, 13, 13, 13, 13, 14, 14, 28, 39, 50, 50, 50, 13, 8, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 13, 13, 28, 28, 39, 39, 50, 50, 50, 13, 13, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 55, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344395916 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001344395916 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344395916/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344395916/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344395916 Building ZINC001344395916 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344395916' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344395916 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001344395916 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344395916/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344395916 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 290) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/290: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)CCNC(N)=O)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001344395916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001344395916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344395916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001344395916 none CCO[C@@H]1CN(C(=O)CCNC(N)=O)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 16, 16, 16, 16, 16, 16, 18, 18, 30, 39, 50, 50, 50, 16, 10, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 16, 16, 30, 30, 39, 39, 50, 50, 50, 16, 16, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 55, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344395916 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344395916/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344395916 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 291) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/291: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)CCNC(N)=O)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001344395916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001344395916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344395916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001344395916 none CCO[C@@H]1CN(C(=O)CCNC(N)=O)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 13, 13, 13, 13, 13, 13, 14, 14, 28, 39, 50, 50, 50, 13, 8, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 13, 13, 28, 28, 39, 39, 50, 50, 50, 13, 13, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 55, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344395916 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001344395916 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344395916/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344395916/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344395916 Building ZINC001344419211 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344419211' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344419211 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001344419211 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344419211/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344419211 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/292 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@@H]2CCC(=O)N2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001344419211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001344419211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344419211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001344419211 none CCO[C@@H]1CN(C(=O)[C@@H]2CCC(=O)N2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 34, 34, 34, 34, 37, 39, 50, 50, 50, 50, 50, 50, 34, 17, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 34, 34, 50, 50, 50, 50, 50, 34, 34, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344419211 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344419211/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344419211 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 293) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/293 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/293' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@@H]2CCC(=O)N2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001344419211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001344419211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344419211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001344419211 none CCO[C@@H]1CN(C(=O)[C@@H]2CCC(=O)N2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 30, 30, 30, 30, 30, 35, 39, 50, 50, 50, 50, 50, 50, 30, 17, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 30, 30, 50, 50, 50, 50, 50, 30, 30, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344419211 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001344419211 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344419211/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344419211/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344419211 Building ZINC001344419211 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344419211' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344419211 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001344419211 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344419211/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344419211 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 292) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/292: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@@H]2CCC(=O)N2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001344419211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001344419211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344419211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001344419211 none CCO[C@@H]1CN(C(=O)[C@@H]2CCC(=O)N2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 34, 34, 34, 34, 37, 39, 50, 50, 50, 50, 50, 50, 34, 17, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 34, 34, 50, 50, 50, 50, 50, 34, 34, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344419211 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344419211/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344419211 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 293) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/293: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@@H]2CCC(=O)N2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001344419211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001344419211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344419211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001344419211 none CCO[C@@H]1CN(C(=O)[C@@H]2CCC(=O)N2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 30, 30, 30, 30, 30, 35, 39, 50, 50, 50, 50, 50, 50, 30, 17, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 30, 30, 50, 50, 50, 50, 50, 30, 30, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [46, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344419211 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001344419211 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344419211/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344419211/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344419211 Building ZINC001344428810 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428810' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428810 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001344428810 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428810/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428810 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/294 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@@H]2CNC(=O)N2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001344428810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001344428810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001344428810 none CCO[C@@H]1CN(C(=O)[C@@H]2CNC(=O)N2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 34, 34, 34, 34, 41, 41, 50, 50, 50, 50, 50, 50, 34, 17, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 34, 34, 50, 50, 50, 50, 34, 34, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 52, 21, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428810 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428810/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428810 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 295) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/295 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/295' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@@H]2CNC(=O)N2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001344428810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001344428810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001344428810 none CCO[C@@H]1CN(C(=O)[C@@H]2CNC(=O)N2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 36, 36, 36, 36, 36, 42, 42, 50, 50, 50, 50, 50, 50, 36, 20, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 36, 36, 50, 50, 50, 50, 36, 36, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 52, 21, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428810 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001344428810 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428810/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428810/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428810 Building ZINC001344428810 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428810' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428810 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001344428810 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428810/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428810 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 294) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/294: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@@H]2CNC(=O)N2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001344428810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001344428810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001344428810 none CCO[C@@H]1CN(C(=O)[C@@H]2CNC(=O)N2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 34, 34, 34, 34, 41, 41, 50, 50, 50, 50, 50, 50, 34, 17, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 34, 34, 50, 50, 50, 50, 34, 34, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 52, 21, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428810 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428810/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428810 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 295) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/295: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@@H]2CNC(=O)N2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001344428810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001344428810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001344428810 none CCO[C@@H]1CN(C(=O)[C@@H]2CNC(=O)N2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 36, 36, 36, 36, 36, 42, 42, 50, 50, 50, 50, 50, 50, 36, 20, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 36, 36, 50, 50, 50, 50, 36, 36, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 52, 21, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428810 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001344428810 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428810/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428810/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428810 Building ZINC001344428811 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428811' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428811 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001344428811 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428811/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428811 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/296 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@H]2CNC(=O)N2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001344428811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001344428811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001344428811 none CCO[C@@H]1CN(C(=O)[C@H]2CNC(=O)N2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 30, 30, 30, 30, 30, 37, 37, 50, 50, 50, 50, 50, 50, 30, 16, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 30, 30, 50, 50, 50, 50, 30, 30, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 52, 21, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428811 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428811/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428811 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 297) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/297 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/297' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@H]2CNC(=O)N2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001344428811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001344428811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001344428811 none CCO[C@@H]1CN(C(=O)[C@H]2CNC(=O)N2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 29, 29, 29, 29, 36, 36, 50, 50, 50, 50, 50, 50, 29, 18, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 29, 29, 50, 50, 50, 50, 29, 29, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 52, 21, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428811 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001344428811 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428811/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428811/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428811 Building ZINC001344428811 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428811' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428811 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001344428811 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428811/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428811 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 296) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/296: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@H]2CNC(=O)N2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001344428811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001344428811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001344428811 none CCO[C@@H]1CN(C(=O)[C@H]2CNC(=O)N2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 30, 30, 30, 30, 30, 37, 37, 50, 50, 50, 50, 50, 50, 30, 16, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 30, 30, 50, 50, 50, 50, 30, 30, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 52, 21, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428811 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428811/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428811 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 297) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/297: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@H]2CNC(=O)N2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001344428811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001344428811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001344428811 none CCO[C@@H]1CN(C(=O)[C@H]2CNC(=O)N2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 29, 29, 29, 29, 36, 36, 50, 50, 50, 50, 50, 50, 29, 18, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 29, 29, 50, 50, 50, 50, 29, 29, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 52, 21, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428811 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001344428811 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428811/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428811/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344428811 Building ZINC001344437563 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344437563' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344437563 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001344437563 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344437563/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344437563 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/298 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)Cn2cncn2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001344437563.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001344437563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344437563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001344437563 none CCO[C@@H]1CN(C(=O)Cn2cncn2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 17, 17, 17, 17, 17, 17, 18, 18, 45, 50, 50, 50, 50, 17, 11, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 17, 17, 45, 45, 50, 50, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344437563 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344437563/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344437563 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 299) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/299 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/299' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)Cn2cncn2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001344437563.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001344437563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344437563/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001344437563 none CCO[C@@H]1CN(C(=O)Cn2cncn2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 19, 19, 19, 19, 19, 19, 20, 20, 45, 50, 50, 50, 50, 19, 10, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 19, 19, 45, 45, 50, 50, 19, 19, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344437563 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001344437563 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344437563/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344437563/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344437563 Building ZINC001344437563 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344437563' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344437563 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001344437563 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344437563/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344437563 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 298) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/298: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)Cn2cncn2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001344437563.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001344437563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344437563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001344437563 none CCO[C@@H]1CN(C(=O)Cn2cncn2)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 17, 17, 17, 17, 17, 17, 18, 18, 45, 50, 50, 50, 50, 17, 11, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 17, 17, 45, 45, 50, 50, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344437563 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344437563/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344437563 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 299) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/299: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)Cn2cncn2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001344437563.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001344437563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344437563/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001344437563 none CCO[C@@H]1CN(C(=O)Cn2cncn2)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 19, 19, 19, 19, 19, 19, 20, 20, 45, 50, 50, 50, 50, 19, 10, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 19, 19, 45, 45, 50, 50, 19, 19, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344437563 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001344437563 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344437563/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344437563/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344437563 Building ZINC001344768746 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344768746' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344768746 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001344768746 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344768746/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344768746 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/300 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cn1ncn(C)c1=O) `ZINC001344768746.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001344768746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344768746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001344768746 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cn1ncn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 8, 1, 8, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 33, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 33, 33, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 152 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344768746 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344768746/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344768746 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 301) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/301 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/301' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cn1ncn(C)c1=O) `ZINC001344768746.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001344768746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344768746/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001344768746 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cn1ncn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 8, 1, 8, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 13, 13, 36, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 36, 36, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344768746 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001344768746 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344768746/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344768746/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344768746 Building ZINC001344768746 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344768746' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344768746 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001344768746 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344768746/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344768746 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 300) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/300: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cn1ncn(C)c1=O) `ZINC001344768746.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001344768746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344768746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001344768746 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cn1ncn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 8, 1, 8, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 33, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 33, 33, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 152 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344768746 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344768746/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344768746 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 301) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/301: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cn1ncn(C)c1=O) `ZINC001344768746.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001344768746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344768746/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001344768746 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cn1ncn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 8, 1, 8, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 13, 13, 36, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 36, 36, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344768746 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001344768746 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344768746/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344768746/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001344768746 Building ZINC001345023298 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345023298' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345023298 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001345023298 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345023298/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345023298 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/302 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)N1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC001345023298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001345023298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345023298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001345023298 none C[C@H](NC(N)=O)C(=O)N1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 49, 49, 50, 50, 50, 17, 33, 17, 17, 17, 17, 17, 17, 9, 1, 12, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 49, 49, 49, 50, 50, 50, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 176 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345023298 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345023298/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345023298 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 303) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/303 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/303' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)N1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC001345023298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001345023298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345023298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001345023298 none C[C@H](NC(N)=O)C(=O)N1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 48, 48, 50, 50, 50, 18, 36, 18, 18, 18, 18, 18, 18, 11, 1, 13, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 48, 48, 48, 50, 50, 50, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 167 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345023298 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001345023298 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345023298/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345023298/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345023298 Building ZINC001345023298 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345023298' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345023298 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001345023298 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345023298/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345023298 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 302) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/302: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)N1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC001345023298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001345023298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345023298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001345023298 none C[C@H](NC(N)=O)C(=O)N1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 49, 49, 50, 50, 50, 17, 33, 17, 17, 17, 17, 17, 17, 9, 1, 12, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 49, 49, 49, 50, 50, 50, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 176 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345023298 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345023298/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345023298 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 303) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/303: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)N1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC001345023298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001345023298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345023298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001345023298 none C[C@H](NC(N)=O)C(=O)N1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 48, 48, 50, 50, 50, 18, 36, 18, 18, 18, 18, 18, 18, 11, 1, 13, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 48, 48, 48, 50, 50, 50, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 167 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345023298 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001345023298 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345023298/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345023298/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345023298 Building ZINC001345273022 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273022' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273022 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001345273022 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273022/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273022 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/304 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCO[C@@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)C1) `ZINC001345273022.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001345273022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001345273022 none CC(=O)N1CCO[C@@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 50, 47, 47, 47, 47, 23, 47, 13, 23, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 47, 50, 50, 50, 47, 47, 47, 47, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 47, 47] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 147 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273022 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273022/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273022 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 305) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/305 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/305' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCO[C@@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)C1) `ZINC001345273022.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001345273022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001345273022 none CC(=O)N1CCO[C@@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 48, 48, 48, 48, 24, 48, 13, 24, 13, 13, 13, 3, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 48, 50, 50, 50, 48, 48, 48, 48, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 48, 48] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 149 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273022 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001345273022 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273022/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273022/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273022 Building ZINC001345273022 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273022' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273022 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001345273022 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273022/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273022 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 304) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/304: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCO[C@@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)C1) `ZINC001345273022.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001345273022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001345273022 none CC(=O)N1CCO[C@@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 50, 47, 47, 47, 47, 23, 47, 13, 23, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 47, 50, 50, 50, 47, 47, 47, 47, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 47, 47] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 147 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273022 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273022/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273022 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 305) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/305: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCO[C@@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)C1) `ZINC001345273022.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001345273022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001345273022 none CC(=O)N1CCO[C@@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 48, 48, 48, 48, 24, 48, 13, 24, 13, 13, 13, 3, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 48, 50, 50, 50, 48, 48, 48, 48, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 48, 48] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 149 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273022 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001345273022 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273022/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273022/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273022 Building ZINC001345273023 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273023' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273023 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001345273023 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273023/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273023 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/306 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCO[C@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)C1) `ZINC001345273023.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001345273023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001345273023 none CC(=O)N1CCO[C@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 50, 46, 46, 46, 46, 21, 46, 11, 21, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 46, 50, 50, 50, 46, 46, 46, 46, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 46, 46] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 143 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273023 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273023/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273023 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 307) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/307 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/307' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCO[C@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)C1) `ZINC001345273023.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001345273023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273023/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001345273023 none CC(=O)N1CCO[C@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 50, 47, 47, 47, 47, 24, 47, 13, 24, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 47, 50, 50, 50, 47, 47, 47, 47, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 47, 47] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 147 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273023 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001345273023 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273023/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273023/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273023 Building ZINC001345273023 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273023' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273023 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001345273023 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273023/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273023 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 306) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/306: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCO[C@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)C1) `ZINC001345273023.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001345273023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001345273023 none CC(=O)N1CCO[C@H](C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 50, 46, 46, 46, 46, 21, 46, 11, 21, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 46, 50, 50, 50, 46, 46, 46, 46, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 46, 46] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 143 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273023 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273023/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273023 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 307) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/307: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCO[C@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)C1) `ZINC001345273023.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001345273023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273023/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001345273023 none CC(=O)N1CCO[C@H](C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 50, 47, 47, 47, 47, 24, 47, 13, 24, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 47, 50, 50, 50, 47, 47, 47, 47, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 47, 47] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53, 54]) total number of confs: 147 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273023 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001345273023 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273023/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273023/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345273023 Building ZINC001345274157 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274157' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274157 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001345274157 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274157/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274157 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/308 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CCS(=O)(=O)N1) `ZINC001345274157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001345274157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001345274157 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CCS(=O)(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.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, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 14, 11, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 27, 39, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 133 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274157 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274157/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274157 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 309) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/309 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/309' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CCS(=O)(=O)N1) `ZINC001345274157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001345274157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001345274157 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CCS(=O)(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.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, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 14, 11, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 26, 41, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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/323031/xbw-8058115.49/working/building/ZINC001345274157 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001345274157 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274157/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274157/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274157 Building ZINC001345274157 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274157' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274157 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001345274157 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274157/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274157 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 308) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/308: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CCS(=O)(=O)N1) `ZINC001345274157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001345274157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001345274157 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CCS(=O)(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.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, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 14, 11, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 27, 39, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 133 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274157 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274157/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274157 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 309) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/309: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CCS(=O)(=O)N1) `ZINC001345274157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001345274157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001345274157 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@H]1CCS(=O)(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.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, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 14, 11, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 26, 41, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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/323031/xbw-8058115.49/working/building/ZINC001345274157 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001345274157 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274157/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274157/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274157 Building ZINC001345274159 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274159' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274159 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001345274159 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274159/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274159 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/310 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CCS(=O)(=O)N1) `ZINC001345274159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001345274159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001345274159 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CCS(=O)(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.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, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 14, 11, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 28, 38, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 137 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274159 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274159/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274159 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 311) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/311 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/311' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CCS(=O)(=O)N1) `ZINC001345274159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001345274159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001345274159 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CCS(=O)(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.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, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 14, 11, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 31, 41, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 135 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274159 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001345274159 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274159/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274159/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274159 Building ZINC001345274159 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274159' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274159 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001345274159 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274159/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274159 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 310) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/310: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CCS(=O)(=O)N1) `ZINC001345274159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001345274159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001345274159 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CCS(=O)(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.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, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 14, 11, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 28, 38, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 137 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274159 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274159/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274159 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 311) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/311: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CCS(=O)(=O)N1) `ZINC001345274159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001345274159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001345274159 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CCS(=O)(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.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, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 14, 11, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 31, 41, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 135 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274159 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001345274159 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274159/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274159/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274159 Building ZINC001345274672 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274672' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274672 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001345274672 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274672/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274672 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/312 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN(C)S(C)(=O)=O) `ZINC001345274672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001345274672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001345274672 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN(C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 14, 5, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 15, 15, 40, 50, 50, 50, 50, 50, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 40, 40, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 189 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274672 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274672/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274672 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 313) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/313 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/313' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN(C)S(C)(=O)=O) `ZINC001345274672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001345274672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001345274672 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN(C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 14, 5, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 17, 17, 38, 50, 50, 50, 50, 50, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 38, 38, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 191 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274672 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001345274672 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274672/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274672/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274672 Building ZINC001345274672 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274672' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274672 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001345274672 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274672/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274672 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 312) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/312: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN(C)S(C)(=O)=O) `ZINC001345274672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001345274672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001345274672 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN(C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 14, 5, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 15, 15, 40, 50, 50, 50, 50, 50, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 40, 40, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 189 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274672 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274672/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274672 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 313) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/313: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN(C)S(C)(=O)=O) `ZINC001345274672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001345274672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001345274672 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN(C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 14, 5, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 17, 17, 38, 50, 50, 50, 50, 50, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 38, 38, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 191 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274672 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001345274672 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274672/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274672/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345274672 Building ZINC001345354102 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345354102' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345354102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001345354102 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345354102/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345354102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/314 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H](CC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1C)C(N)=O) `ZINC001345354102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001345354102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345354102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001345354102 none CC(=O)N[C@@H](CC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1C)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 1, 8, 11, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 44, 42, 44, 19, 19, 19, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 44, 50, 50, 50, 50, 50, 50, 42, 42, 19, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345354102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345354102/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345354102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 315) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/315 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/315' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H](CC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1C)C(N)=O) `ZINC001345354102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001345354102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345354102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001345354102 none CC(=O)N[C@@H](CC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1C)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 1, 8, 11, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 42, 41, 42, 19, 19, 19, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 42, 49, 49, 50, 50, 50, 50, 41, 41, 19, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 49, 49] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 207 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345354102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001345354102 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345354102/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345354102/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345354102 Building ZINC001345354102 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345354102' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345354102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001345354102 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345354102/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345354102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 314) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/314: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H](CC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1C)C(N)=O) `ZINC001345354102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001345354102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345354102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001345354102 none CC(=O)N[C@@H](CC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1C)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 1, 8, 11, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 44, 42, 44, 19, 19, 19, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 44, 50, 50, 50, 50, 50, 50, 42, 42, 19, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345354102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345354102/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345354102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 315) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/315: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@H](CC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1C)C(N)=O) `ZINC001345354102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001345354102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345354102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001345354102 none CC(=O)N[C@@H](CC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1C)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 1, 8, 11, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 42, 41, 42, 19, 19, 19, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 42, 49, 49, 50, 50, 50, 50, 41, 41, 19, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 49, 49] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 207 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345354102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001345354102 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345354102/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345354102/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345354102 Building ZINC001345733297 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345733297' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345733297 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001345733297 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345733297/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345733297 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/316 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCO)C1CCN(C(=O)[C@H]2C[C@H]2C(N)=O)CC1) `ZINC001345733297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001345733297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345733297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001345733297 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCO)C1CCN(C(=O)[C@H]2C[C@H]2C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 9, 3, 5, 5, 5, 5, 14, 14, 28, 28, 28, 28, 28, 41, 41, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 9, 9, 27, 5, 5, 5, 5, 5, 28, 28, 41, 41, 5, 5, 5, 5] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 201 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345733297 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345733297/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345733297 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 317) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/317 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/317' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCO)C1CCN(C(=O)[C@H]2C[C@H]2C(N)=O)CC1) `ZINC001345733297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001345733297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345733297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001345733297 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCO)C1CCN(C(=O)[C@H]2C[C@H]2C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 8, 4, 6, 6, 6, 6, 17, 17, 29, 29, 29, 29, 29, 43, 43, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 8, 8, 24, 6, 6, 6, 6, 6, 29, 29, 43, 43, 6, 6, 6, 6] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 189 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345733297 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001345733297 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345733297/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345733297/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345733297 Building ZINC001345733297 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345733297' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345733297 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001345733297 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345733297/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345733297 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 316) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/316: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCO)C1CCN(C(=O)[C@H]2C[C@H]2C(N)=O)CC1) `ZINC001345733297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001345733297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345733297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001345733297 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCO)C1CCN(C(=O)[C@H]2C[C@H]2C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 9, 3, 5, 5, 5, 5, 14, 14, 28, 28, 28, 28, 28, 41, 41, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 9, 9, 27, 5, 5, 5, 5, 5, 28, 28, 41, 41, 5, 5, 5, 5] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 201 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345733297 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345733297/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345733297 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 317) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/317: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCO)C1CCN(C(=O)[C@H]2C[C@H]2C(N)=O)CC1) `ZINC001345733297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001345733297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345733297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001345733297 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCO)C1CCN(C(=O)[C@H]2C[C@H]2C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 8, 4, 6, 6, 6, 6, 17, 17, 29, 29, 29, 29, 29, 43, 43, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 8, 8, 24, 6, 6, 6, 6, 6, 29, 29, 43, 43, 6, 6, 6, 6] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 189 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345733297 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001345733297 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345733297/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345733297/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001345733297 Building ZINC001346021055 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346021055' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346021055 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001346021055 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346021055/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346021055 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/318 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CN2CCOCC2=O)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001346021055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001346021055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346021055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001346021055 none C[C@@H]1CN(C(=O)CN2CCOCC2=O)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 5, 5, 12, 5, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 30, 30, 48, 50, 50, 50, 50, 50, 50, 28, 13, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 48, 48, 50, 50, 50, 50, 50, 50, 28, 28, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346021055 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346021055/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346021055 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 319) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/319 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/319' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CN2CCOCC2=O)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001346021055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001346021055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346021055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001346021055 none C[C@@H]1CN(C(=O)CN2CCOCC2=O)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 5, 5, 12, 5, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 29, 29, 44, 50, 50, 50, 50, 50, 50, 28, 16, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 44, 44, 50, 50, 50, 50, 50, 50, 28, 28, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346021055 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001346021055 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346021055/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346021055/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346021055 Building ZINC001346021055 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346021055' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346021055 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001346021055 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346021055/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346021055 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 318) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/318: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CN2CCOCC2=O)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001346021055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001346021055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346021055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001346021055 none C[C@@H]1CN(C(=O)CN2CCOCC2=O)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 5, 5, 12, 5, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 30, 30, 48, 50, 50, 50, 50, 50, 50, 28, 13, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 48, 48, 50, 50, 50, 50, 50, 50, 28, 28, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346021055 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346021055/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346021055 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 319) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/319: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CN2CCOCC2=O)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001346021055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001346021055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346021055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001346021055 none C[C@@H]1CN(C(=O)CN2CCOCC2=O)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 5, 5, 12, 5, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 29, 29, 44, 50, 50, 50, 50, 50, 50, 28, 16, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 44, 44, 50, 50, 50, 50, 50, 50, 28, 28, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346021055 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001346021055 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346021055/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346021055/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346021055 Building ZINC001346117586 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346117586' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346117586 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001346117586 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346117586/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346117586 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/320 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N(C)CC(=O)NC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1C) `ZINC001346117586.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001346117586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346117586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001346117586 none COCC(=O)N(C)CC(=O)NC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 28, 21, 28, 13, 21, 3, 3, 3, 3, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50, 50, 50, 50, 21, 21, 21, 13, 13, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346117586 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346117586/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346117586 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 321) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/321 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/321' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N(C)CC(=O)NC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1C) `ZINC001346117586.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001346117586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346117586/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001346117586 none COCC(=O)N(C)CC(=O)NC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 29, 25, 29, 17, 25, 5, 5, 5, 5, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 25, 25, 25, 17, 17, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346117586 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001346117586 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346117586/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346117586/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346117586 Building ZINC001346117586 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346117586' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346117586 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001346117586 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346117586/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346117586 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 320) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/320: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N(C)CC(=O)NC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1C) `ZINC001346117586.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001346117586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346117586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001346117586 none COCC(=O)N(C)CC(=O)NC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 28, 21, 28, 13, 21, 3, 3, 3, 3, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50, 50, 50, 50, 21, 21, 21, 13, 13, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346117586 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346117586/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346117586 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 321) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/321: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N(C)CC(=O)NC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1C) `ZINC001346117586.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001346117586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346117586/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001346117586 none COCC(=O)N(C)CC(=O)NC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 29, 25, 29, 17, 25, 5, 5, 5, 5, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 25, 25, 25, 17, 17, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346117586 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001346117586 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346117586/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346117586/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346117586 Building ZINC001346202109 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001346202109 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/322 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1) `ZINC001346202109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001346202109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001346202109 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 22, 22, 22, 46, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 39, 39, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 323) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/323 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/323' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1) `ZINC001346202109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001346202109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001346202109 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 22, 22, 22, 46, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 39, 39, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 324) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/324 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/324' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1) `ZINC001346202109.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001346202109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001346202109 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 44, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 35, 35, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 325) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/325 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/325' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1) `ZINC001346202109.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001346202109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001346202109 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 44, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 35, 35, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001346202109 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 Building ZINC001346202109 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001346202109 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 322) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/322: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1) `ZINC001346202109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001346202109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001346202109 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 22, 22, 22, 46, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 39, 39, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 323) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/323: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1) `ZINC001346202109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001346202109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001346202109 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 22, 22, 22, 46, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 39, 39, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 324) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/324: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1) `ZINC001346202109.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001346202109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001346202109 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 44, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 35, 35, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 325) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/325: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1) `ZINC001346202109.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001346202109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001346202109 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 44, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 35, 35, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001346202109 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 Building ZINC001346202109 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001346202109 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 322) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/322: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1) `ZINC001346202109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001346202109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001346202109 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 22, 22, 22, 46, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 39, 39, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 323) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/323: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1) `ZINC001346202109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001346202109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001346202109 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 22, 22, 22, 46, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 39, 39, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 324) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/324: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1) `ZINC001346202109.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001346202109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001346202109 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 44, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 35, 35, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 325) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/325: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1) `ZINC001346202109.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001346202109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001346202109 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 44, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 35, 35, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001346202109 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 Building ZINC001346202109 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001346202109 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 322) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/322: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1) `ZINC001346202109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001346202109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001346202109 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 22, 22, 22, 46, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 39, 39, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 323) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/323: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1) `ZINC001346202109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001346202109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001346202109 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 22, 22, 22, 46, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 39, 39, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 324) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/324: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1) `ZINC001346202109.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001346202109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001346202109 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 44, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 35, 35, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 325) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/325: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1) `ZINC001346202109.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001346202109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001346202109 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CN1CCNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 44, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 35, 35, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001346202109 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346202109 Building ZINC001346231543 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346231543' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346231543 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001346231543 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346231543/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346231543 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/326 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CCn1cnnn1) `ZINC001346231543.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001346231543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346231543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001346231543 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CCn1cnnn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', '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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 17, 17, 17, 40, 46, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 17, 40, 40, 46, 46, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346231543 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346231543/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346231543 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 327) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/327 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/327' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CCn1cnnn1) `ZINC001346231543.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001346231543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346231543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001346231543 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CCn1cnnn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', '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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 37, 44, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 37, 37, 44, 44, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346231543 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001346231543 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346231543/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346231543/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346231543 Building ZINC001346231543 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346231543' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346231543 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001346231543 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346231543/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346231543 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 326) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/326: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CCn1cnnn1) `ZINC001346231543.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001346231543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346231543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001346231543 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CCn1cnnn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', '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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 17, 17, 17, 40, 46, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 17, 40, 40, 46, 46, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346231543 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346231543/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346231543 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 327) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/327: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CCn1cnnn1) `ZINC001346231543.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001346231543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346231543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001346231543 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CCn1cnnn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', '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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 37, 44, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 37, 37, 44, 44, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([50, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346231543 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001346231543 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346231543/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346231543/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346231543 Building ZINC001346377592 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346377592' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346377592 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001346377592 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346377592/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346377592 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/328 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)Cn2cnnn2)C[C@H]1CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001346377592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001346377592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346377592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001346377592 none C[C@@H]1CN(C(=O)Cn2cnnn2)C[C@H]1CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 8, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 20, 20, 37, 50, 50, 50, 50, 18, 12, 18, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 37, 37, 50, 18, 18, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346377592 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346377592/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346377592 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 329) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/329 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/329' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)Cn2cnnn2)C[C@H]1CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001346377592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001346377592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346377592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001346377592 none C[C@@H]1CN(C(=O)Cn2cnnn2)C[C@H]1CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 8, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 18, 18, 46, 50, 50, 50, 50, 16, 13, 16, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 46, 46, 50, 16, 16, 9, 9, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346377592 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001346377592 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346377592/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346377592/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346377592 Building ZINC001346377592 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346377592' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346377592 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001346377592 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346377592/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346377592 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 328) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/328: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)Cn2cnnn2)C[C@H]1CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001346377592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001346377592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346377592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001346377592 none C[C@@H]1CN(C(=O)Cn2cnnn2)C[C@H]1CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 8, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 20, 20, 37, 50, 50, 50, 50, 18, 12, 18, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 37, 37, 50, 18, 18, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346377592 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346377592/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346377592 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 329) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/329: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)Cn2cnnn2)C[C@H]1CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001346377592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001346377592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346377592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001346377592 none C[C@@H]1CN(C(=O)Cn2cnnn2)C[C@H]1CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 8, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 18, 18, 46, 50, 50, 50, 50, 16, 13, 16, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 46, 46, 50, 16, 16, 9, 9, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346377592 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001346377592 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346377592/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346377592/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346377592 Building ZINC001346926251 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346926251' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346926251 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001346926251 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346926251/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346926251 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/330 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/330' -> `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]1C[C@H]2CC[C@@H]1N2C(=O)CN1C(=O)CCC1=O) `ZINC001346926251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001346926251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346926251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001346926251 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)CN1C(=O)CCC1=O NO_LONG_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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 11, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 30, 30, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 170 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346926251 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346926251/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346926251 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 331) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/331 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/331' -> `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]1C[C@H]2CC[C@@H]1N2C(=O)CN1C(=O)CCC1=O) `ZINC001346926251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001346926251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346926251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001346926251 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)CN1C(=O)CCC1=O NO_LONG_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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 11, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 34, 34, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 159 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346926251 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001346926251 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346926251/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346926251/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346926251 Building ZINC001346926251 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346926251' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346926251 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001346926251 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346926251/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346926251 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 330) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/330: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)CN1C(=O)CCC1=O) `ZINC001346926251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001346926251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346926251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001346926251 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)CN1C(=O)CCC1=O NO_LONG_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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 11, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 30, 30, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 170 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346926251 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346926251/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346926251 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 331) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/331: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)CN1C(=O)CCC1=O) `ZINC001346926251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001346926251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346926251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001346926251 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)CN1C(=O)CCC1=O NO_LONG_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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 8, 1, 11, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 34, 34, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 159 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346926251 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001346926251 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346926251/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346926251/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346926251 Building ZINC001346927576 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346927576' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346927576 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001346927576 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346927576/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346927576 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/332 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/332' -> `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]1C[C@H]2CC[C@@H]1N2C(=O)[C@H]1CC[C@@H](C(N)=O)O1) `ZINC001346927576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001346927576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346927576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001346927576 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 20, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 39, 34, 35, 36, 6, 5, 37, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 137 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346927576 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346927576/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346927576 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 333) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/333 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/333' -> `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]1C[C@H]2CC[C@@H]1N2C(=O)[C@H]1CC[C@@H](C(N)=O)O1) `ZINC001346927576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001346927576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346927576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001346927576 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 21, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 39, 34, 35, 36, 6, 5, 37, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 135 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346927576 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001346927576 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346927576/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346927576/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346927576 Building ZINC001346927576 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346927576' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346927576 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001346927576 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346927576/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346927576 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 332) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/332: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@H]1CC[C@@H](C(N)=O)O1) `ZINC001346927576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001346927576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346927576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001346927576 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 20, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 39, 34, 35, 36, 6, 5, 37, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 137 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346927576 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346927576/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346927576 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 333) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/333: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@H]1CC[C@@H](C(N)=O)O1) `ZINC001346927576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001346927576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346927576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001346927576 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 21, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 39, 34, 35, 36, 6, 5, 37, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 135 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346927576 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001346927576 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346927576/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346927576/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001346927576 Building ZINC001347297535 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347297535' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347297535 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001347297535 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347297535/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347297535 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/334 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)NC(C)(C)C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001347297535.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001347297535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347297535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001347297535 none CN(CC(=O)NC(C)(C)C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 15, 15, 15, 15, 15, 15, 1, 2, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 5, 5, 5, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 8, 8, 2, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347297535 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347297535/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347297535 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 335) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/335 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/335' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)NC(C)(C)C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001347297535.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001347297535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347297535/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001347297535 none CN(CC(=O)NC(C)(C)C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 15, 15, 15, 15, 15, 15, 1, 2, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 5, 5, 5, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 8, 8, 2, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347297535 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001347297535 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347297535/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347297535/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347297535 Building ZINC001347297535 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347297535' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347297535 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001347297535 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347297535/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347297535 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 334) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/334: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)NC(C)(C)C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001347297535.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001347297535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347297535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001347297535 none CN(CC(=O)NC(C)(C)C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 15, 15, 15, 15, 15, 15, 1, 2, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 5, 5, 5, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 8, 8, 2, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347297535 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347297535/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347297535 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 335) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/335: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)NC(C)(C)C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001347297535.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001347297535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347297535/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001347297535 none CN(CC(=O)NC(C)(C)C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 15, 15, 15, 15, 15, 15, 1, 2, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 5, 5, 5, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 8, 8, 2, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347297535 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001347297535 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347297535/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347297535/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347297535 Building ZINC001347460451 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347460451' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347460451 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001347460451 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347460451/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347460451 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/336 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/336' -> `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]1C[C@H]2CC[C@@H]1N2C(=O)C[C@@H]1NC(=O)NC1=O) `ZINC001347460451.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001347460451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347460451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001347460451 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@@H]1NC(=O)NC1=O NO_LONG_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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 7, 8, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 20, 20, 42, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 42, 42, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 193 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347460451 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347460451/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347460451 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 337) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/337 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/337' -> `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]1C[C@H]2CC[C@@H]1N2C(=O)C[C@@H]1NC(=O)NC1=O) `ZINC001347460451.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001347460451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347460451/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001347460451 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@@H]1NC(=O)NC1=O NO_LONG_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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 7, 8, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 15, 15, 41, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 41, 41, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 189 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347460451 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001347460451 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347460451/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347460451/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347460451 Building ZINC001347460451 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347460451' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347460451 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001347460451 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347460451/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347460451 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 336) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/336: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@@H]1NC(=O)NC1=O) `ZINC001347460451.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001347460451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347460451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001347460451 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@@H]1NC(=O)NC1=O NO_LONG_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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 7, 8, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 20, 20, 42, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 42, 42, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 193 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347460451 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347460451/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347460451 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 337) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/337: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@@H]1NC(=O)NC1=O) `ZINC001347460451.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001347460451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347460451/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001347460451 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C[C@@H]1NC(=O)NC1=O NO_LONG_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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 7, 8, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 4, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 15, 15, 41, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 41, 41, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 189 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347460451 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001347460451 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347460451/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347460451/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347460451 Building ZINC001347597934 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001347597934 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/338 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21) `ZINC001347597934.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001347597934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001347597934 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 12, 5, 5, 7, 5, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 25, 39, 45, 39, 39, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 18, 18, 45, 45, 135, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 291 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 339) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/339 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/339' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21) `ZINC001347597934.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001347597934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001347597934 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 12, 5, 5, 7, 5, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 20, 36, 41, 36, 36, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 41, 41, 123, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 266 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 340) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/340 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/340' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21) `ZINC001347597934.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001347597934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001347597934 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 12, 5, 5, 7, 5, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 25, 39, 45, 39, 39, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 18, 18, 45, 45, 135, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 291 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 341) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/341 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/341' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21) `ZINC001347597934.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001347597934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001347597934 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 12, 5, 5, 7, 5, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 20, 36, 41, 36, 36, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 41, 41, 123, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 266 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001347597934 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 Building ZINC001347597934 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001347597934 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 338) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/338: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21) `ZINC001347597934.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001347597934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001347597934 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 12, 5, 5, 7, 5, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 25, 39, 45, 39, 39, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 18, 18, 45, 45, 135, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 291 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 339) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/339: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21) `ZINC001347597934.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001347597934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001347597934 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 12, 5, 5, 7, 5, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 20, 36, 41, 36, 36, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 41, 41, 123, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 266 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 340) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/340: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21) `ZINC001347597934.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001347597934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001347597934 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 12, 5, 5, 7, 5, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 25, 39, 45, 39, 39, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 18, 18, 45, 45, 135, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 291 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 341) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/341: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21) `ZINC001347597934.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001347597934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001347597934 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 12, 5, 5, 7, 5, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 20, 36, 41, 36, 36, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 41, 41, 123, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 266 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001347597934 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 Building ZINC001347597934 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001347597934 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 338) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/338: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21) `ZINC001347597934.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001347597934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001347597934 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 12, 5, 5, 7, 5, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 25, 39, 45, 39, 39, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 18, 18, 45, 45, 135, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 291 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 339) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/339: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21) `ZINC001347597934.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001347597934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001347597934 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 12, 5, 5, 7, 5, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 20, 36, 41, 36, 36, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 41, 41, 123, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 266 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 340) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/340: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21) `ZINC001347597934.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001347597934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001347597934 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 12, 5, 5, 7, 5, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 25, 39, 45, 39, 39, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 18, 18, 45, 45, 135, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 291 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 341) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/341: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21) `ZINC001347597934.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001347597934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001347597934 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 12, 5, 5, 7, 5, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 20, 36, 41, 36, 36, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 41, 41, 123, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 266 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001347597934 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 Building ZINC001347597934 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001347597934 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 338) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/338: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21) `ZINC001347597934.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001347597934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001347597934 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 12, 5, 5, 7, 5, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 25, 39, 45, 39, 39, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 18, 18, 45, 45, 135, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 291 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 339) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/339: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21) `ZINC001347597934.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001347597934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001347597934 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 12, 5, 5, 7, 5, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 20, 36, 41, 36, 36, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 41, 41, 123, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 266 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 340) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/340: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21) `ZINC001347597934.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001347597934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001347597934 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 12, 5, 5, 7, 5, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 25, 39, 45, 39, 39, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 18, 18, 45, 45, 135, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 291 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 341) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/341: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21) `ZINC001347597934.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001347597934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001347597934 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@]1(CO)COC[C@@H]2CCCN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 12, 5, 5, 7, 5, 5, 5, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 20, 36, 41, 36, 36, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 41, 41, 123, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 266 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001347597934 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347597934 Building ZINC001347599742 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347599742' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347599742 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001347599742 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347599742/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347599742 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/342 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)NCC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001347599742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001347599742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347599742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001347599742 none CCS(=O)(=O)NCC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 50, 50, 43, 19, 19, 19, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 44, 43, 43, 19, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 187 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347599742 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347599742/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347599742 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 343) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/343 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/343' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)NCC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001347599742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001347599742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347599742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001347599742 none CCS(=O)(=O)NCC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 50, 40, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 42, 40, 40, 15, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347599742 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001347599742 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347599742/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347599742/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347599742 Building ZINC001347599742 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347599742' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347599742 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001347599742 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347599742/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347599742 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 342) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/342: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)NCC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001347599742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001347599742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347599742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001347599742 none CCS(=O)(=O)NCC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 50, 50, 43, 19, 19, 19, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 44, 43, 43, 19, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 187 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347599742 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347599742/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347599742 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 343) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/343: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)NCC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001347599742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001347599742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347599742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001347599742 none CCS(=O)(=O)NCC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 50, 40, 15, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 42, 40, 40, 15, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347599742 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001347599742 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347599742/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347599742/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347599742 Building ZINC001347754140 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754140' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001347754140 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754140/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/344 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC(F)(F)C[C@@H]1CO) `ZINC001347754140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001347754140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001347754140 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC(F)(F)C[C@@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 5, 5, 7, 5, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 14, 4, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 16, 4, 4, 4, 4, 14, 14, 4, 12, 12, 12, 12, 16, 16, 48] 150 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]) total number of confs: 137 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754140/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 345) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/345 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/345' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC(F)(F)C[C@@H]1CO) `ZINC001347754140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001347754140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001347754140 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC(F)(F)C[C@@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 5, 5, 7, 5, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 10, 4, 1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 15, 4, 4, 4, 4, 10, 10, 4, 10, 10, 10, 10, 15, 15, 45] 150 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]) total number of confs: 120 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001347754140 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754140/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754140/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754140 Building ZINC001347754140 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754140' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001347754140 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754140/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 344) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/344: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC(F)(F)C[C@@H]1CO) `ZINC001347754140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001347754140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001347754140 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC(F)(F)C[C@@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 5, 5, 7, 5, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 14, 4, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 16, 4, 4, 4, 4, 14, 14, 4, 12, 12, 12, 12, 16, 16, 48] 150 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]) total number of confs: 137 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754140/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 345) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/345: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC(F)(F)C[C@@H]1CO) `ZINC001347754140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001347754140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001347754140 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC(F)(F)C[C@@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 5, 5, 7, 5, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 10, 4, 1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 15, 4, 4, 4, 4, 10, 10, 4, 10, 10, 10, 10, 15, 15, 45] 150 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]) total number of confs: 120 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001347754140 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754140/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754140/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754140 Building ZINC001347754141 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754141' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001347754141 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754141/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/346 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC(F)(F)C[C@H]1CO) `ZINC001347754141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001347754141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001347754141 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC(F)(F)C[C@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 5, 5, 7, 5, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 12, 4, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 14, 4, 4, 4, 4, 12, 12, 4, 8, 8, 8, 8, 14, 14, 42] 150 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]) total number of confs: 129 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754141/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 347) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/347 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/347' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC(F)(F)C[C@H]1CO) `ZINC001347754141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001347754141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001347754141 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC(F)(F)C[C@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 5, 5, 7, 5, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 14, 4, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 16, 4, 4, 4, 4, 14, 14, 4, 12, 12, 12, 12, 16, 16, 48] 150 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]) total number of confs: 137 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001347754141 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754141/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754141/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754141 Building ZINC001347754141 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754141' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001347754141 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754141/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 346) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/346: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC(F)(F)C[C@H]1CO) `ZINC001347754141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001347754141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001347754141 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC(F)(F)C[C@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 5, 5, 7, 5, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 12, 4, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 14, 4, 4, 4, 4, 12, 12, 4, 8, 8, 8, 8, 14, 14, 42] 150 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]) total number of confs: 129 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754141/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 347) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/347: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC(F)(F)C[C@H]1CO) `ZINC001347754141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001347754141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001347754141 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC(F)(F)C[C@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 5, 5, 7, 5, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 14, 4, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 16, 4, 4, 4, 4, 14, 14, 4, 12, 12, 12, 12, 16, 16, 48] 150 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]) total number of confs: 137 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001347754141 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754141/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754141/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347754141 Building ZINC001347761437 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347761437' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347761437 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001347761437 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347761437/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347761437 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/348 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC(C2CCOCC2)C1) `ZINC001347761437.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001347761437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347761437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001347761437 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC(C2CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 2, 1, 1, 1, 1, 2, 4, 7, 7, 11, 13, 13, 13, 13, 13, 7, 2, 2, 2, 2, 7, 7, 2, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 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, 42, 43, 44]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347761437 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347761437/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347761437 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 349) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/349 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/349' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC(C2CCOCC2)C1) `ZINC001347761437.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001347761437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347761437/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001347761437 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC(C2CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 2, 1, 1, 1, 1, 2, 4, 8, 8, 11, 16, 16, 16, 16, 16, 8, 2, 2, 2, 2, 7, 7, 2, 8, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8] 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, 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/323031/xbw-8058115.49/working/building/ZINC001347761437 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001347761437 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347761437/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347761437/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347761437 Building ZINC001347761437 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347761437' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347761437 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001347761437 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347761437/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347761437 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 348) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/348: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC(C2CCOCC2)C1) `ZINC001347761437.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001347761437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347761437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001347761437 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC(C2CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 2, 1, 1, 1, 1, 2, 4, 7, 7, 11, 13, 13, 13, 13, 13, 7, 2, 2, 2, 2, 7, 7, 2, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 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, 42, 43, 44]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347761437 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347761437/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347761437 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 349) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/349: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC(C2CCOCC2)C1) `ZINC001347761437.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001347761437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347761437/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001347761437 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC(C2CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 2, 1, 1, 1, 1, 2, 4, 8, 8, 11, 16, 16, 16, 16, 16, 8, 2, 2, 2, 2, 7, 7, 2, 8, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8] 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, 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/323031/xbw-8058115.49/working/building/ZINC001347761437 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001347761437 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347761437/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347761437/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347761437 Building ZINC001347832178 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832178' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832178 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001347832178 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832178/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832178 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/350 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](O)C(F)(F)C1) `ZINC001347832178.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001347832178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001347832178 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](O)C(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 6, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 8, 8, 2, 13, 13, 13, 13, 39, 13, 13] 150 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832178 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832178/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832178 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 351) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/351 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/351' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](O)C(F)(F)C1) `ZINC001347832178.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001347832178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001347832178 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](O)C(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 7, 2, 1, 1, 1, 2, 8, 10, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 2, 7, 7, 2, 12, 12, 12, 12, 36, 12, 12] 150 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832178 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001347832178 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832178/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832178/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832178 Building ZINC001347832178 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832178' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832178 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001347832178 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832178/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832178 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 350) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/350: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](O)C(F)(F)C1) `ZINC001347832178.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001347832178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001347832178 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](O)C(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 6, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 8, 8, 2, 13, 13, 13, 13, 39, 13, 13] 150 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832178 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832178/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832178 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 351) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/351: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](O)C(F)(F)C1) `ZINC001347832178.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001347832178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001347832178 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](O)C(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 7, 2, 1, 1, 1, 2, 8, 10, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 2, 7, 7, 2, 12, 12, 12, 12, 36, 12, 12] 150 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832178 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001347832178 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832178/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832178/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832178 Building ZINC001347832180 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832180' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832180 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001347832180 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832180/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832180 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/352 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](O)C(F)(F)C1) `ZINC001347832180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001347832180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001347832180 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](O)C(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 7, 2, 1, 1, 1, 2, 7, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 2, 7, 7, 2, 14, 14, 14, 14, 42, 14, 14] 150 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832180 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832180/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832180 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 353) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/353 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/353' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](O)C(F)(F)C1) `ZINC001347832180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001347832180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001347832180 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](O)C(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 8, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 2, 8, 8, 2, 14, 14, 14, 14, 42, 14, 14] 150 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832180 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001347832180 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832180/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832180/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832180 Building ZINC001347832180 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832180' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832180 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001347832180 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832180/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832180 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 352) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/352: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](O)C(F)(F)C1) `ZINC001347832180.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001347832180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001347832180 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](O)C(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 7, 2, 1, 1, 1, 2, 7, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 2, 7, 7, 2, 14, 14, 14, 14, 42, 14, 14] 150 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832180 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832180/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832180 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 353) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/353: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](O)C(F)(F)C1) `ZINC001347832180.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001347832180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832180/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001347832180 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](O)C(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 8, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 2, 8, 8, 2, 14, 14, 14, 14, 42, 14, 14] 150 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832180 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001347832180 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832180/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832180/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347832180 Building ZINC001347867792 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867792' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867792 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001347867792 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867792/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867792 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/354 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NS(C)(=O)=O)C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001347867792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001347867792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001347867792 none C[C@@H](NS(C)(=O)=O)C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 5, 11, 11, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 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, 7, 7, 6, 6, 7, 6, 4, 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: [44, 16, 44, 44, 49, 50, 50, 50, 16, 16, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 2, 2, 2, 44, 44, 44, 49, 50, 50, 50, 16, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 192 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867792 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867792/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867792 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 355) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/355 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/355' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NS(C)(=O)=O)C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001347867792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001347867792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001347867792 none C[C@@H](NS(C)(=O)=O)C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 5, 11, 11, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 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, 7, 7, 6, 6, 7, 6, 4, 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: [42, 12, 42, 42, 48, 50, 50, 50, 12, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 42, 42, 42, 48, 50, 50, 50, 12, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 192 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867792 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001347867792 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867792/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867792/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867792 Building ZINC001347867792 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867792' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867792 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001347867792 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867792/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867792 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 354) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/354: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NS(C)(=O)=O)C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001347867792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001347867792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001347867792 none C[C@@H](NS(C)(=O)=O)C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 5, 11, 11, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 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, 7, 7, 6, 6, 7, 6, 4, 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: [44, 16, 44, 44, 49, 50, 50, 50, 16, 16, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 2, 2, 2, 44, 44, 44, 49, 50, 50, 50, 16, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 192 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867792 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867792/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867792 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 355) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/355: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NS(C)(=O)=O)C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001347867792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001347867792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001347867792 none C[C@@H](NS(C)(=O)=O)C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 5, 11, 11, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 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, 7, 7, 6, 6, 7, 6, 4, 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: [42, 12, 42, 42, 48, 50, 50, 50, 12, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 42, 42, 42, 48, 50, 50, 50, 12, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 192 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867792 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001347867792 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867792/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867792/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867792 Building ZINC001347867793 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867793' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867793 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001347867793 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867793/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867793 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/356 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NS(C)(=O)=O)C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001347867793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001347867793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001347867793 none C[C@H](NS(C)(=O)=O)C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 5, 11, 11, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 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, 7, 7, 6, 6, 7, 6, 4, 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: [45, 14, 45, 45, 50, 50, 50, 50, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 45, 45, 45, 50, 50, 50, 50, 14, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 182 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867793 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867793/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867793 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 357) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/357 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/357' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NS(C)(=O)=O)C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001347867793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001347867793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001347867793 none C[C@H](NS(C)(=O)=O)C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 5, 11, 11, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 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, 7, 7, 6, 6, 7, 6, 4, 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: [38, 12, 38, 38, 48, 50, 50, 50, 12, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 38, 38, 38, 48, 50, 50, 50, 12, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 186 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867793 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001347867793 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867793/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867793/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867793 Building ZINC001347867793 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867793' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867793 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001347867793 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867793/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867793 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 356) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/356: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NS(C)(=O)=O)C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001347867793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001347867793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001347867793 none C[C@H](NS(C)(=O)=O)C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 5, 11, 11, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 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, 7, 7, 6, 6, 7, 6, 4, 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: [45, 14, 45, 45, 50, 50, 50, 50, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 45, 45, 45, 50, 50, 50, 50, 14, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 182 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867793 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867793/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867793 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 357) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/357: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NS(C)(=O)=O)C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001347867793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001347867793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001347867793 none C[C@H](NS(C)(=O)=O)C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 5, 11, 11, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 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, 7, 7, 6, 6, 7, 6, 4, 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: [38, 12, 38, 38, 48, 50, 50, 50, 12, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 38, 38, 38, 48, 50, 50, 50, 12, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 186 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867793 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001347867793 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867793/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867793/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001347867793 Building ZINC001348455158 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001348455158 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/358 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)C2)cn1) `ZINC001348455158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001348455158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455158 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 7, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 13, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 60, 13, 13, 6] 150 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 359) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/359 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/359' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)C2)cn1) `ZINC001348455158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001348455158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455158 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 12, 12, 6, 6, 1, 1, 1, 1, 6, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 12, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 23, 69, 12, 12, 6] 150 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 181 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 360) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/360 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/360' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)C2)cn1) `ZINC001348455158.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001348455158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455158 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 7, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 13, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 60, 13, 13, 6] 150 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 361) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/361 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/361' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)C2)cn1) `ZINC001348455158.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001348455158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455158 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 12, 12, 6, 6, 1, 1, 1, 1, 6, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 12, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 23, 69, 12, 12, 6] 150 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 181 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001348455158 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 Building ZINC001348455158 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001348455158 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 358) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/358: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)C2)cn1) `ZINC001348455158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001348455158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455158 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 7, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 13, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 60, 13, 13, 6] 150 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 359) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/359: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)C2)cn1) `ZINC001348455158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001348455158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455158 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 12, 12, 6, 6, 1, 1, 1, 1, 6, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 12, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 23, 69, 12, 12, 6] 150 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 181 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 360) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/360: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)C2)cn1) `ZINC001348455158.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001348455158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455158 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 7, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 13, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 60, 13, 13, 6] 150 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 361) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)C2)cn1) `ZINC001348455158.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001348455158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455158 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 12, 12, 6, 6, 1, 1, 1, 1, 6, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 12, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 23, 69, 12, 12, 6] 150 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 181 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001348455158 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 Building ZINC001348455158 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001348455158 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 358) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/358: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)C2)cn1) `ZINC001348455158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001348455158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455158 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 7, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 13, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 60, 13, 13, 6] 150 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 359) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/359: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)C2)cn1) `ZINC001348455158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001348455158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455158 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 12, 12, 6, 6, 1, 1, 1, 1, 6, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 12, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 23, 69, 12, 12, 6] 150 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 181 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 360) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/360: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)C2)cn1) `ZINC001348455158.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001348455158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455158 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 7, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 13, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 60, 13, 13, 6] 150 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 361) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)C2)cn1) `ZINC001348455158.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001348455158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455158 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 12, 12, 6, 6, 1, 1, 1, 1, 6, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 12, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 23, 69, 12, 12, 6] 150 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 181 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001348455158 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 Building ZINC001348455158 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001348455158 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 358) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/358: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)C2)cn1) `ZINC001348455158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001348455158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455158 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 7, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 13, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 60, 13, 13, 6] 150 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 359) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/359: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)C2)cn1) `ZINC001348455158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001348455158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455158 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 12, 12, 6, 6, 1, 1, 1, 1, 6, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 12, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 23, 69, 12, 12, 6] 150 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 181 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 360) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/360: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)C2)cn1) `ZINC001348455158.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001348455158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455158 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 7, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 13, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 20, 20, 60, 13, 13, 6] 150 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 361) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)C2)cn1) `ZINC001348455158.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001348455158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455158 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 12, 12, 6, 6, 1, 1, 1, 1, 6, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 12, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 23, 69, 12, 12, 6] 150 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 181 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001348455158 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455158 Building ZINC001348455161 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001348455161 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/362 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)C2)cn1) `ZINC001348455161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001348455161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455161 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 20, 20, 10, 10, 1, 1, 1, 2, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 21, 9, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 21, 21, 63, 9, 9, 10] 150 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 199 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 363) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/363 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/363' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)C2)cn1) `ZINC001348455161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001348455161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455161 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 20, 20, 11, 11, 1, 1, 1, 2, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 19, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 19, 19, 57, 11, 11, 11] 150 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 364) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/364 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/364' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)C2)cn1) `ZINC001348455161.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001348455161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455161 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 20, 20, 10, 10, 1, 1, 1, 2, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 21, 9, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 21, 21, 63, 9, 9, 10] 150 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 199 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 365) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/365 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/365' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)C2)cn1) `ZINC001348455161.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001348455161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455161 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 20, 20, 11, 11, 1, 1, 1, 2, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 19, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 19, 19, 57, 11, 11, 11] 150 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001348455161 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 Building ZINC001348455161 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001348455161 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 362) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/362: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)C2)cn1) `ZINC001348455161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001348455161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455161 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 20, 20, 10, 10, 1, 1, 1, 2, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 21, 9, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 21, 21, 63, 9, 9, 10] 150 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 199 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 363) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/363: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)C2)cn1) `ZINC001348455161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001348455161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455161 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 20, 20, 11, 11, 1, 1, 1, 2, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 19, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 19, 19, 57, 11, 11, 11] 150 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 364) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/364: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)C2)cn1) `ZINC001348455161.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001348455161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455161 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 20, 20, 10, 10, 1, 1, 1, 2, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 21, 9, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 21, 21, 63, 9, 9, 10] 150 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 199 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 365) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/365: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)C2)cn1) `ZINC001348455161.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001348455161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455161 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 20, 20, 11, 11, 1, 1, 1, 2, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 19, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 19, 19, 57, 11, 11, 11] 150 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001348455161 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 Building ZINC001348455161 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001348455161 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 362) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/362: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)C2)cn1) `ZINC001348455161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001348455161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455161 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 20, 20, 10, 10, 1, 1, 1, 2, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 21, 9, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 21, 21, 63, 9, 9, 10] 150 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 199 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 363) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/363: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)C2)cn1) `ZINC001348455161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001348455161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455161 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 20, 20, 11, 11, 1, 1, 1, 2, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 19, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 19, 19, 57, 11, 11, 11] 150 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 364) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/364: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)C2)cn1) `ZINC001348455161.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001348455161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455161 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 20, 20, 10, 10, 1, 1, 1, 2, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 21, 9, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 21, 21, 63, 9, 9, 10] 150 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 199 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 365) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/365: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)C2)cn1) `ZINC001348455161.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001348455161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455161 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 20, 20, 11, 11, 1, 1, 1, 2, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 19, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 19, 19, 57, 11, 11, 11] 150 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001348455161 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 Building ZINC001348455161 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001348455161 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 362) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/362: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)C2)cn1) `ZINC001348455161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001348455161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455161 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 20, 20, 10, 10, 1, 1, 1, 2, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 21, 9, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 21, 21, 63, 9, 9, 10] 150 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 199 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 363) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/363: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)C2)cn1) `ZINC001348455161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001348455161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455161 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 20, 20, 11, 11, 1, 1, 1, 2, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 19, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 19, 19, 57, 11, 11, 11] 150 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 364) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/364: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)C2)cn1) `ZINC001348455161.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001348455161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455161 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 20, 20, 10, 10, 1, 1, 1, 2, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 21, 9, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 21, 21, 63, 9, 9, 10] 150 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 199 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 365) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/365: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)C2)cn1) `ZINC001348455161.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001348455161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001348455161 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCN3CCOC[C@]3(CO)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', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 12, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 20, 20, 11, 11, 1, 1, 1, 2, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 19, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 19, 19, 57, 11, 11, 11] 150 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 176 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001348455161 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348455161 Building ZINC001348491139 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491139' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491139 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001348491139 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491139/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491139 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/366 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN([C@@]2(C(=O)O)CCOC2)CC1) `ZINC001348491139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001348491139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001348491139 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN([C@@]2(C(=O)O)CCOC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 12, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 17, 17, 17, 20, 35, 36, 36, 35, 35, 35, 35, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 108, 35, 35, 35, 35, 35, 35, 17, 17, 17, 17] 144 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 194 number of broken/clashed sets: 112 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491139 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491139/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491139 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 367) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/367 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/367' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN([C@@]2(C(=O)O)CCOC2)CC1) `ZINC001348491139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001348491139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001348491139 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN([C@@]2(C(=O)O)CCOC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 12, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 15, 15, 15, 17, 36, 37, 37, 36, 36, 36, 36, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 111, 36, 36, 36, 36, 36, 36, 15, 15, 15, 15] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 203 number of broken/clashed sets: 111 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491139 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001348491139 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491139/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491139/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491139 Building ZINC001348491139 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491139' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491139 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001348491139 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491139/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491139 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 366) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/366: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN([C@@]2(C(=O)O)CCOC2)CC1) `ZINC001348491139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001348491139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001348491139 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN([C@@]2(C(=O)O)CCOC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 12, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 17, 17, 17, 20, 35, 36, 36, 35, 35, 35, 35, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 108, 35, 35, 35, 35, 35, 35, 17, 17, 17, 17] 144 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 194 number of broken/clashed sets: 112 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491139 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491139/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491139 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 367) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/367: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN([C@@]2(C(=O)O)CCOC2)CC1) `ZINC001348491139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001348491139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001348491139 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN([C@@]2(C(=O)O)CCOC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 12, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 15, 15, 15, 17, 36, 37, 37, 36, 36, 36, 36, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 111, 36, 36, 36, 36, 36, 36, 15, 15, 15, 15] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 203 number of broken/clashed sets: 111 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491139 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001348491139 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491139/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491139/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491139 Building ZINC001348491140 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491140' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001348491140 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491140/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/368 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN([C@]2(C(=O)O)CCOC2)CC1) `ZINC001348491140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001348491140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001348491140 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN([C@]2(C(=O)O)CCOC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 12, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 17, 17, 17, 20, 38, 39, 39, 38, 38, 38, 38, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 117, 38, 38, 38, 38, 38, 38, 17, 17, 17, 17] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 215 number of broken/clashed sets: 117 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491140/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 369) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/369 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/369' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN([C@]2(C(=O)O)CCOC2)CC1) `ZINC001348491140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001348491140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001348491140 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN([C@]2(C(=O)O)CCOC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 12, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 15, 15, 15, 17, 37, 39, 39, 37, 37, 37, 37, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 117, 37, 37, 37, 37, 37, 37, 15, 15, 15, 15] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 218 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001348491140 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491140/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491140/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491140 Building ZINC001348491140 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491140' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001348491140 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491140/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 368) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/368: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN([C@]2(C(=O)O)CCOC2)CC1) `ZINC001348491140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001348491140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001348491140 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN([C@]2(C(=O)O)CCOC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 12, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 17, 17, 17, 20, 38, 39, 39, 38, 38, 38, 38, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 117, 38, 38, 38, 38, 38, 38, 17, 17, 17, 17] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 215 number of broken/clashed sets: 117 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491140/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 369) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/369: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN([C@]2(C(=O)O)CCOC2)CC1) `ZINC001348491140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001348491140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001348491140 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN([C@]2(C(=O)O)CCOC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 12, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 15, 15, 15, 17, 37, 39, 39, 37, 37, 37, 37, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 117, 37, 37, 37, 37, 37, 37, 15, 15, 15, 15] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 218 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001348491140 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491140/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491140/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001348491140 Building ZINC001350989672 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350989672' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350989672 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001350989672 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350989672/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350989672 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/370 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CN(C)C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cnn1C) `ZINC001350989672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001350989672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350989672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001350989672 none Cc1c(CN(C)C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cnn1C 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', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 15, 5, 2, 5, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 20, 20, 20, 20, 20, 20, 20, 15, 15, 5, 5, 5, 2, 5, 5, 2, 2, 2, 2, 20, 20, 20, 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350989672 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350989672/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350989672 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 371) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/371 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/371' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CN(C)C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cnn1C) `ZINC001350989672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001350989672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350989672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001350989672 none Cc1c(CN(C)C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cnn1C 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', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 15, 5, 2, 5, 1, 2, 1, 1, 1, 2, 2, 2, 6, 6, 6, 2, 2, 2, 20, 20, 20, 20, 20, 20, 20, 15, 15, 5, 5, 5, 2, 6, 6, 2, 2, 2, 2, 20, 20, 20, 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350989672 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001350989672 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350989672/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350989672/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350989672 Building ZINC001350989672 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350989672' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350989672 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001350989672 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350989672/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350989672 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 370) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/370: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CN(C)C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cnn1C) `ZINC001350989672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001350989672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350989672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001350989672 none Cc1c(CN(C)C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cnn1C 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', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 15, 5, 2, 5, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 20, 20, 20, 20, 20, 20, 20, 15, 15, 5, 5, 5, 2, 5, 5, 2, 2, 2, 2, 20, 20, 20, 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350989672 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350989672/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350989672 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 371) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/371: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CN(C)C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cnn1C) `ZINC001350989672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001350989672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350989672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001350989672 none Cc1c(CN(C)C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)cnn1C 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', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', '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'] dock atom type numbers: [5, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 15, 5, 2, 5, 1, 2, 1, 1, 1, 2, 2, 2, 6, 6, 6, 2, 2, 2, 20, 20, 20, 20, 20, 20, 20, 15, 15, 5, 5, 5, 2, 6, 6, 2, 2, 2, 2, 20, 20, 20, 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350989672 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001350989672 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350989672/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350989672/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350989672 Building ZINC001350991683 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991683' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991683 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001350991683 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991683/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991683 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/372 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](O)CC(F)(F)C1) `ZINC001350991683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001350991683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001350991683 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](O)CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 9, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 8, 8, 2, 11, 11, 33, 11, 11, 11, 11] 150 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991683 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991683/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991683 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 373) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/373 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/373' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H](O)CC(F)(F)C1) `ZINC001350991683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001350991683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001350991683 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H](O)CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 7, 2, 1, 1, 1, 2, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 2, 7, 7, 2, 12, 12, 36, 12, 12, 12, 12] 150 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991683 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001350991683 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991683/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991683/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991683 Building ZINC001350991683 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991683' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991683 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001350991683 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991683/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991683 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 372) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/372: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](O)CC(F)(F)C1) `ZINC001350991683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001350991683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001350991683 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](O)CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 9, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 8, 8, 2, 11, 11, 33, 11, 11, 11, 11] 150 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991683 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991683/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991683 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 373) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/373: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H](O)CC(F)(F)C1) `ZINC001350991683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001350991683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001350991683 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1C[C@H](O)CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 7, 2, 1, 1, 1, 2, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 2, 7, 7, 2, 12, 12, 36, 12, 12, 12, 12] 150 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991683 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001350991683 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991683/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991683/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991683 Building ZINC001350991689 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991689' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991689 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001350991689 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991689/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991689 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/374 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)CC(F)(F)C1) `ZINC001350991689.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001350991689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001350991689 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 1, 6, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 2, 8, 8, 2, 14, 14, 42, 14, 14, 14, 14] 150 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991689 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991689/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991689 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 375) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/375 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/375' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)CC(F)(F)C1) `ZINC001350991689.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001350991689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991689/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001350991689 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 6, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 8, 8, 2, 13, 13, 39, 13, 13, 13, 13] 150 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991689 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001350991689 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991689/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991689/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991689 Building ZINC001350991689 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991689' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991689 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001350991689 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991689/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991689 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 374) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/374: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)CC(F)(F)C1) `ZINC001350991689.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001350991689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001350991689 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 1, 6, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 2, 8, 8, 2, 14, 14, 42, 14, 14, 14, 14] 150 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991689 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991689/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991689 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 375) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/375: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)CC(F)(F)C1) `ZINC001350991689.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001350991689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991689/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001350991689 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 6, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 8, 8, 2, 13, 13, 39, 13, 13, 13, 13] 150 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991689 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001350991689 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991689/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991689/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001350991689 Building ZINC001351002197 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002197' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002197 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001351002197 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002197/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002197 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/376 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@]2(CCCOC2)C1) `ZINC001351002197.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001351002197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001351002197 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@]2(CCCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 2, 1, 1, 1, 2, 5, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 7, 7, 2, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002197 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002197/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002197 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 377) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/377 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/377' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@]2(CCCOC2)C1) `ZINC001351002197.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001351002197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002197/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001351002197 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@]2(CCCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 2, 1, 1, 1, 2, 4, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 7, 7, 2, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002197 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001351002197 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002197/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002197/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002197 Building ZINC001351002197 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002197' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002197 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001351002197 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002197/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002197 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 376) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/376: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@]2(CCCOC2)C1) `ZINC001351002197.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001351002197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001351002197 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@]2(CCCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 2, 1, 1, 1, 2, 5, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 7, 7, 2, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002197 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002197/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002197 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 377) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/377: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@]2(CCCOC2)C1) `ZINC001351002197.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001351002197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002197/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001351002197 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@]2(CCCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 2, 1, 1, 1, 2, 4, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 7, 7, 2, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002197 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001351002197 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002197/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002197/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002197 Building ZINC001351002199 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002199' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002199 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001351002199 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002199/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002199 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/378 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@]2(CCCOC2)C1) `ZINC001351002199.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001351002199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001351002199 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@]2(CCCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 5, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 2, 2, 2, 2, 8, 8, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002199 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002199/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002199 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 379) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/379 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/379' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@]2(CCCOC2)C1) `ZINC001351002199.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001351002199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002199/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001351002199 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@]2(CCCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 2, 1, 1, 1, 2, 3, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 7, 7, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002199 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001351002199 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002199/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002199/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002199 Building ZINC001351002199 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002199' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002199 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001351002199 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002199/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002199 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 378) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/378: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@]2(CCCOC2)C1) `ZINC001351002199.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001351002199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001351002199 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@]2(CCCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 5, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 2, 2, 2, 2, 8, 8, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002199 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002199/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002199 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 379) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/379: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@]2(CCCOC2)C1) `ZINC001351002199.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001351002199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002199/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001351002199 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@]2(CCCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 2, 1, 1, 1, 2, 3, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 7, 7, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002199 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001351002199 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002199/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002199/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001351002199 Building ZINC001356582102 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001356582102' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001356582102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001356582102 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001356582102/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001356582102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/380 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C1CC1) `ZINC001356582102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001356582102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001356582102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001356582102 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 14, 24, 29, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 14, 14, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 188 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001356582102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001356582102/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001356582102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 381) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/381 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/381' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C1CC1) `ZINC001356582102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001356582102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001356582102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001356582102 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 16, 25, 30, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 16, 16, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 188 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001356582102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001356582102 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001356582102/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001356582102/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001356582102 Building ZINC001356582102 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001356582102' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001356582102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001356582102 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001356582102/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001356582102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 380) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/380: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C1CC1) `ZINC001356582102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001356582102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001356582102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001356582102 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN(C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 14, 24, 29, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 14, 14, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 188 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001356582102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001356582102/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001356582102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 381) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/381: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C1CC1) `ZINC001356582102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001356582102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001356582102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001356582102 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN(C(=O)[C@H]1CC[C@@H](C(N)=O)O1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 16, 25, 30, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 16, 16, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 188 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001356582102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001356582102 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001356582102/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001356582102/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001356582102 Building ZINC001357398799 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398799' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398799 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357398799 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398799/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398799 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/382 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12) `ZINC001357398799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357398799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001357398799 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 20, 20, 19, 34, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 60, 34, 34, 44, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 274 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398799 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398799/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398799 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 383) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/383 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/383' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12) `ZINC001357398799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357398799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001357398799 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 13, 27, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 42, 27, 27, 41, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 245 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398799 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001357398799 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398799/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398799/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398799 Building ZINC001357398799 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398799' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398799 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357398799 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398799/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398799 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 382) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/382: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12) `ZINC001357398799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357398799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001357398799 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 20, 20, 19, 34, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 60, 34, 34, 44, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 274 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398799 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398799/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398799 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 383) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/383: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12) `ZINC001357398799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357398799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001357398799 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](O)CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 13, 27, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 42, 27, 27, 41, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 245 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398799 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001357398799 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398799/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398799/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398799 Building ZINC001357398800 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398800' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398800 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357398800 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398800/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398800 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/384 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12) `ZINC001357398800.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357398800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001357398800 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 13, 13, 13, 27, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 39, 27, 27, 40, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 243 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398800 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398800/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398800 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 385) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/385 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/385' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12) `ZINC001357398800.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357398800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001357398800 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 21, 21, 21, 36, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 63, 36, 36, 48, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 274 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398800 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001357398800 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398800/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398800/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398800 Building ZINC001357398800 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398800' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398800 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001357398800 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398800/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398800 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 384) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/384: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12) `ZINC001357398800.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001357398800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001357398800 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 13, 13, 13, 27, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 39, 27, 27, 40, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 243 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398800 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398800/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398800 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 385) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/385: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12) `ZINC001357398800.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001357398800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001357398800 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](O)CNC(=O)[C@@H]1OC[C@@H]2COCC[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 21, 21, 21, 36, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 63, 36, 36, 48, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 274 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398800 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001357398800 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398800/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398800/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001357398800 Building ZINC001358834289 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834289' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834289 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358834289 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834289/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834289 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/386 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001358834289.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358834289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001358834289 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 24, 24, 24, 24, 24, 28, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 24, 24, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834289 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834289/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834289 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 387) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/387 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/387' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001358834289.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358834289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834289/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001358834289 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 24, 24, 24, 24, 24, 29, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 24, 24, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834289 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001358834289 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834289/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834289/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834289 Building ZINC001358834289 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834289' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834289 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358834289 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834289/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834289 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 386) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/386: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001358834289.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358834289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001358834289 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 24, 24, 24, 24, 24, 28, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 24, 24, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834289 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834289/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834289 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 387) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/387: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001358834289.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358834289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834289/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001358834289 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 24, 24, 24, 24, 24, 29, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 24, 24, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834289 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001358834289 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834289/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834289/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834289 Building ZINC001358834290 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834290' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834290 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358834290 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834290/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834290 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/388 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001358834290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358834290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001358834290 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 29, 29, 29, 29, 29, 35, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 153 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834290 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834290/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834290 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 389) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/389 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/389' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001358834290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358834290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001358834290 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 24, 24, 24, 24, 24, 28, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 24, 24, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834290 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001358834290 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834290/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834290/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834290 Building ZINC001358834290 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834290' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834290 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001358834290 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834290/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834290 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 388) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/388: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001358834290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001358834290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001358834290 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 29, 29, 29, 29, 29, 35, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 153 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834290 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834290/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834290 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 389) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/389: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001358834290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001358834290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001358834290 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 24, 24, 24, 24, 24, 28, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 24, 24, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834290 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001358834290 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834290/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834290/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001358834290 Building ZINC001435685136 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685136' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685136 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435685136 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685136/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685136 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/390 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@@]3(CCS(=O)(=O)C3)C2)cn1) `ZINC001435685136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435685136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001435685136 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@@]3(CCS(=O)(=O)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 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, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 7, 14, 14, 14, 14, 14, 7, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685136 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685136/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685136 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 391) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/391 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/391' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@@]3(CCS(=O)(=O)C3)C2)cn1) `ZINC001435685136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435685136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001435685136 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@@]3(CCS(=O)(=O)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 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, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 15, 15, 15, 15, 15, 6, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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/323031/xbw-8058115.49/working/building/ZINC001435685136 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001435685136 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685136/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685136/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685136 Building ZINC001435685136 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685136' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685136 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435685136 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685136/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685136 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 390) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/390: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@@]3(CCS(=O)(=O)C3)C2)cn1) `ZINC001435685136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435685136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001435685136 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@@]3(CCS(=O)(=O)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 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, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 7, 14, 14, 14, 14, 14, 7, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685136 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685136/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685136 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 391) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/391: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@@]3(CCS(=O)(=O)C3)C2)cn1) `ZINC001435685136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435685136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001435685136 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@@]3(CCS(=O)(=O)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 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, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 15, 15, 15, 15, 15, 6, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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/323031/xbw-8058115.49/working/building/ZINC001435685136 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001435685136 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685136/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685136/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685136 Building ZINC001435685138 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685138' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685138 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435685138 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685138/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685138 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/392 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@]3(CCS(=O)(=O)C3)C2)cn1) `ZINC001435685138.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435685138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001435685138 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@]3(CCS(=O)(=O)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 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, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 7, 17, 17, 17, 17, 17, 7, 3, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685138 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685138/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685138 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 393) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/393 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/393' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@]3(CCS(=O)(=O)C3)C2)cn1) `ZINC001435685138.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435685138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685138/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001435685138 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@]3(CCS(=O)(=O)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 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, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 14, 14, 14, 14, 14, 6, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685138 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001435685138 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685138/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685138/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685138 Building ZINC001435685138 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685138' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685138 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435685138 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685138/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685138 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 392) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/392: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@]3(CCS(=O)(=O)C3)C2)cn1) `ZINC001435685138.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435685138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001435685138 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@]3(CCS(=O)(=O)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 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, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 7, 17, 17, 17, 17, 17, 7, 3, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685138 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685138/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685138 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 393) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/393: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@]3(CCS(=O)(=O)C3)C2)cn1) `ZINC001435685138.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435685138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685138/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001435685138 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCO[C@]3(CCS(=O)(=O)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 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, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 14, 14, 14, 14, 14, 6, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685138 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001435685138 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685138/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685138/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685138 Building ZINC001435685143 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685143' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685143 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435685143 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685143/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685143 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/394 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@]3(CCS(=O)(=O)C3)C2)cn1) `ZINC001435685143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435685143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001435685143 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@]3(CCS(=O)(=O)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 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, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 12, 12, 12, 12, 12, 6, 3, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685143 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685143/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685143 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 395) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/395 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/395' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@]3(CCS(=O)(=O)C3)C2)cn1) `ZINC001435685143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435685143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001435685143 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@]3(CCS(=O)(=O)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 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, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 15, 15, 15, 15, 15, 6, 2, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685143 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001435685143 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685143/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685143/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685143 Building ZINC001435685143 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685143' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685143 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435685143 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685143/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685143 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 394) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/394: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@]3(CCS(=O)(=O)C3)C2)cn1) `ZINC001435685143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435685143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001435685143 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@]3(CCS(=O)(=O)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 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, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 12, 12, 12, 12, 12, 6, 3, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685143 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685143/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685143 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 395) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/395: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@]3(CCS(=O)(=O)C3)C2)cn1) `ZINC001435685143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435685143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001435685143 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@]3(CCS(=O)(=O)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 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, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 15, 15, 15, 15, 15, 6, 2, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685143 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001435685143 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685143/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685143/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685143 Building ZINC001435685149 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685149' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685149 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435685149 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685149/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685149 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/396 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@@]3(CCS(=O)(=O)C3)C2)cn1) `ZINC001435685149.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435685149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001435685149 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@@]3(CCS(=O)(=O)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 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, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 7, 7, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 7, 13, 13, 13, 13, 13, 7, 2, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 82 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685149 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685149/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685149 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 397) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/397 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/397' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@@]3(CCS(=O)(=O)C3)C2)cn1) `ZINC001435685149.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435685149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685149/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001435685149 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@@]3(CCS(=O)(=O)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 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, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 14, 14, 14, 14, 14, 6, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 91 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685149 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001435685149 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685149/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685149/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685149 Building ZINC001435685149 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685149' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685149 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435685149 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685149/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685149 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 396) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/396: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@@]3(CCS(=O)(=O)C3)C2)cn1) `ZINC001435685149.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435685149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001435685149 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@@]3(CCS(=O)(=O)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 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, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 7, 7, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 7, 13, 13, 13, 13, 13, 7, 2, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 82 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685149 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685149/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685149 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 397) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/397: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@@]3(CCS(=O)(=O)C3)C2)cn1) `ZINC001435685149.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435685149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685149/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001435685149 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCO[C@@]3(CCS(=O)(=O)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 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, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 14, 14, 14, 14, 14, 6, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 91 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685149 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001435685149 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685149/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685149/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435685149 Building ZINC001435756167 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435756167' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435756167 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435756167 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435756167/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435756167 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/398 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccn(CCS(C)(=O)=O)c2=O)cn1) `ZINC001435756167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435756167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435756167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001435756167 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccn(CCS(C)(=O)=O)c2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 14, 5, 11, 11, 1, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 7, 13, 13, 30, 30, 30, 7, 7, 8, 8, 8, 8, 8, 8, 4, 7, 7, 7, 13, 13, 13, 13, 30, 30, 30, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435756167 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435756167/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435756167 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 399) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/399 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/399' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2cccn(CCS(C)(=O)=O)c2=O)cn1) `ZINC001435756167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435756167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435756167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001435756167 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2cccn(CCS(C)(=O)=O)c2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 14, 5, 11, 11, 1, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 7, 13, 13, 29, 29, 29, 7, 7, 8, 8, 8, 8, 8, 8, 4, 7, 7, 7, 13, 13, 13, 13, 29, 29, 29, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435756167 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001435756167 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435756167/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435756167/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435756167 Building ZINC001435756167 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435756167' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435756167 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435756167 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435756167/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435756167 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 398) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/398: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccn(CCS(C)(=O)=O)c2=O)cn1) `ZINC001435756167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435756167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435756167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001435756167 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccn(CCS(C)(=O)=O)c2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 14, 5, 11, 11, 1, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 7, 13, 13, 30, 30, 30, 7, 7, 8, 8, 8, 8, 8, 8, 4, 7, 7, 7, 13, 13, 13, 13, 30, 30, 30, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435756167 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435756167/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435756167 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 399) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/399: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2cccn(CCS(C)(=O)=O)c2=O)cn1) `ZINC001435756167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435756167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435756167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001435756167 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2cccn(CCS(C)(=O)=O)c2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 14, 5, 11, 11, 1, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 7, 13, 13, 29, 29, 29, 7, 7, 8, 8, 8, 8, 8, 8, 4, 7, 7, 7, 13, 13, 13, 13, 29, 29, 29, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435756167 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001435756167 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435756167/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435756167/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001435756167 Building ZINC001436738537 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001436738537 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/400 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@@](C)CC2)cn1) `ZINC001436738537.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436738537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001436738537 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 18, 19, 19, 19, 19, 19, 18, 18, 18, 18, 18, 18, 5, 5, 10, 10, 10, 10, 10, 5, 2, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 97 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 401) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/401 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/401' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@@](C)CC2)cn1) `ZINC001436738537.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436738537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001436738537 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 9, 9, 9, 9, 9, 5, 2, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 89 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 402) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/402 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/402' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@](C)CC2)cn1) `ZINC001436738537.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436738537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001436738537 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 18, 19, 19, 19, 19, 19, 18, 18, 18, 18, 18, 18, 5, 5, 10, 10, 10, 10, 10, 5, 2, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 97 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 403) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/403 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/403' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@](C)CC2)cn1) `ZINC001436738537.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436738537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001436738537 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 10, 10, 10, 10, 10, 5, 2, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 94 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001436738537 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 Building ZINC001436738537 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001436738537 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 400) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/400: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@@](C)CC2)cn1) `ZINC001436738537.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436738537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001436738537 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 18, 19, 19, 19, 19, 19, 18, 18, 18, 18, 18, 18, 5, 5, 10, 10, 10, 10, 10, 5, 2, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 97 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 401) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/401: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@@](C)CC2)cn1) `ZINC001436738537.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436738537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001436738537 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 9, 9, 9, 9, 9, 5, 2, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 89 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 402) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/402: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@](C)CC2)cn1) `ZINC001436738537.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436738537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001436738537 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 18, 19, 19, 19, 19, 19, 18, 18, 18, 18, 18, 18, 5, 5, 10, 10, 10, 10, 10, 5, 2, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 97 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 403) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/403: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@](C)CC2)cn1) `ZINC001436738537.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436738537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001436738537 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 10, 10, 10, 10, 10, 5, 2, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 94 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001436738537 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 Building ZINC001436738537 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001436738537 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 400) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/400: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@@](C)CC2)cn1) `ZINC001436738537.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436738537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001436738537 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 18, 19, 19, 19, 19, 19, 18, 18, 18, 18, 18, 18, 5, 5, 10, 10, 10, 10, 10, 5, 2, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 97 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 401) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/401: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@@](C)CC2)cn1) `ZINC001436738537.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436738537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001436738537 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 9, 9, 9, 9, 9, 5, 2, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 89 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 402) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/402: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@](C)CC2)cn1) `ZINC001436738537.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436738537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001436738537 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 18, 19, 19, 19, 19, 19, 18, 18, 18, 18, 18, 18, 5, 5, 10, 10, 10, 10, 10, 5, 2, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 97 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 403) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/403: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@](C)CC2)cn1) `ZINC001436738537.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436738537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001436738537 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 10, 10, 10, 10, 10, 5, 2, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 94 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001436738537 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 Building ZINC001436738537 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001436738537 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 400) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/400: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@@](C)CC2)cn1) `ZINC001436738537.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436738537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001436738537 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 18, 19, 19, 19, 19, 19, 18, 18, 18, 18, 18, 18, 5, 5, 10, 10, 10, 10, 10, 5, 2, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 97 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 401) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/401: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@@](C)CC2)cn1) `ZINC001436738537.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436738537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001436738537 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 9, 9, 9, 9, 9, 5, 2, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 89 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 402) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/402: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@](C)CC2)cn1) `ZINC001436738537.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436738537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001436738537 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 18, 19, 19, 19, 19, 19, 18, 18, 18, 18, 18, 18, 5, 5, 10, 10, 10, 10, 10, 5, 2, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 97 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 403) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/403: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@](C)CC2)cn1) `ZINC001436738537.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436738537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001436738537 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCOCC3)CC[N@](C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 10, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 10, 10, 10, 10, 10, 5, 2, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 94 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001436738537 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001436738537 Building ZINC001438659537 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438659537' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438659537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438659537 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438659537/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438659537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/404 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC1(C(N)=O)CCS(=O)(=O)CC1) `ZINC001438659537.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438659537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438659537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001438659537 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC1(C(N)=O)CCS(=O)(=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', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 11, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 6, 6, 16, 35, 45, 45, 35, 35, 35, 35, 35, 35, 35, 4, 4, 4, 4, 4, 4, 4, 6, 45, 45, 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]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438659537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438659537/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438659537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 405) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/405 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/405' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC1(C(N)=O)CCS(=O)(=O)CC1) `ZINC001438659537.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438659537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438659537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001438659537 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC1(C(N)=O)CCS(=O)(=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', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 11, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 34, 46, 46, 34, 34, 34, 34, 34, 34, 34, 4, 4, 4, 4, 4, 4, 4, 6, 46, 46, 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438659537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001438659537 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438659537/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438659537/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438659537 Building ZINC001438659537 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438659537' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438659537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438659537 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438659537/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438659537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 404) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/404: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC1(C(N)=O)CCS(=O)(=O)CC1) `ZINC001438659537.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438659537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438659537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001438659537 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC1(C(N)=O)CCS(=O)(=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', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 11, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 6, 6, 16, 35, 45, 45, 35, 35, 35, 35, 35, 35, 35, 4, 4, 4, 4, 4, 4, 4, 6, 45, 45, 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]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438659537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438659537/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438659537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 405) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/405: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC1(C(N)=O)CCS(=O)(=O)CC1) `ZINC001438659537.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438659537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438659537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001438659537 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC1(C(N)=O)CCS(=O)(=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', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 11, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 34, 46, 46, 34, 34, 34, 34, 34, 34, 34, 4, 4, 4, 4, 4, 4, 4, 6, 46, 46, 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438659537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001438659537 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438659537/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438659537/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438659537 Building ZINC001438917860 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438917860' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438917860 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438917860 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438917860/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438917860 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/406 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nnc2n1CCNC2=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001438917860.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438917860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438917860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001438917860 none O=C(NCc1nnc2n1CCNC2=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 22, 26, 26, 22, 26, 26, 26, 26, 26, 1, 1, 1, 8, 8, 8, 8, 12, 12, 8, 12, 12, 8, 5, 17, 17, 26, 26, 26, 26, 26, 8, 12, 12, 12, 12, 12, 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, 39, 40, 41]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438917860 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438917860/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438917860 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 407) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/407 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/407' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nnc2n1CCNC2=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001438917860.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438917860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438917860/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001438917860 none O=C(NCc1nnc2n1CCNC2=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 22, 26, 26, 22, 26, 26, 26, 26, 26, 1, 1, 1, 8, 8, 8, 8, 12, 12, 8, 12, 12, 8, 5, 17, 17, 26, 26, 26, 26, 26, 8, 12, 12, 8, 12, 12, 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, 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/323031/xbw-8058115.49/working/building/ZINC001438917860 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001438917860 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438917860/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438917860/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438917860 Building ZINC001438917860 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438917860' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438917860 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438917860 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438917860/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438917860 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 406) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/406: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nnc2n1CCNC2=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001438917860.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438917860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438917860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001438917860 none O=C(NCc1nnc2n1CCNC2=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 22, 26, 26, 22, 26, 26, 26, 26, 26, 1, 1, 1, 8, 8, 8, 8, 12, 12, 8, 12, 12, 8, 5, 17, 17, 26, 26, 26, 26, 26, 8, 12, 12, 12, 12, 12, 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, 39, 40, 41]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438917860 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438917860/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438917860 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 407) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/407: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nnc2n1CCNC2=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001438917860.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438917860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438917860/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001438917860 none O=C(NCc1nnc2n1CCNC2=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 22, 26, 26, 22, 26, 26, 26, 26, 26, 1, 1, 1, 8, 8, 8, 8, 12, 12, 8, 12, 12, 8, 5, 17, 17, 26, 26, 26, 26, 26, 8, 12, 12, 8, 12, 12, 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, 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/323031/xbw-8058115.49/working/building/ZINC001438917860 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001438917860 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438917860/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438917860/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001438917860 Building ZINC001439878653 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878653' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878653 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439878653 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878653/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878653 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/408 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)C(=O)CN1C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001439878653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439878653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001439878653 none COC(=O)[C@H]1CN(C)C(=O)CN1C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 5, 1, 11, 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] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 18, 8, 8, 8, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 9, 9, 9, 4, 18, 18, 18, 8, 8, 8, 8, 8, 8, 8, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878653 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878653/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878653 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 409) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/409 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/409' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)C(=O)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001439878653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439878653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001439878653 none COC(=O)[C@H]1CN(C)C(=O)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 5, 1, 11, 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] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 10, 22, 10, 10, 10, 10, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 7, 7, 7, 6, 22, 22, 22, 10, 10, 10, 10, 10, 10, 10, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878653 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001439878653 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878653/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878653/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878653 Building ZINC001439878653 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878653' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878653 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439878653 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878653/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878653 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 408) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/408: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)C(=O)CN1C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001439878653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439878653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001439878653 none COC(=O)[C@H]1CN(C)C(=O)CN1C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 5, 1, 11, 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] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 18, 8, 8, 8, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 9, 9, 9, 4, 18, 18, 18, 8, 8, 8, 8, 8, 8, 8, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878653 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878653/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878653 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 409) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/409: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)C(=O)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001439878653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439878653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001439878653 none COC(=O)[C@H]1CN(C)C(=O)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 5, 1, 11, 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] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 10, 22, 10, 10, 10, 10, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 7, 7, 7, 6, 22, 22, 22, 10, 10, 10, 10, 10, 10, 10, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878653 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001439878653 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878653/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878653/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878653 Building ZINC001439878945 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878945' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878945 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439878945 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878945/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878945 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/410 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)C(=O)CN1C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001439878945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439878945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001439878945 none COC(=O)[C@@H]1CN(C)C(=O)CN1C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 5, 1, 11, 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] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 21, 9, 9, 9, 9, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 4, 21, 21, 21, 9, 9, 9, 9, 9, 9, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878945 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878945/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878945 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 411) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/411 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/411' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)C(=O)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001439878945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439878945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001439878945 none COC(=O)[C@@H]1CN(C)C(=O)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 5, 1, 11, 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] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 23, 10, 10, 10, 10, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 23, 23, 23, 10, 10, 10, 10, 10, 10, 10, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878945 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001439878945 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878945/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878945/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878945 Building ZINC001439878945 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878945' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878945 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439878945 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878945/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878945 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 410) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/410: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)C(=O)CN1C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001439878945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439878945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001439878945 none COC(=O)[C@@H]1CN(C)C(=O)CN1C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 5, 1, 11, 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] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 21, 9, 9, 9, 9, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 4, 21, 21, 21, 9, 9, 9, 9, 9, 9, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878945 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878945/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878945 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 411) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/411: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)C(=O)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001439878945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439878945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001439878945 none COC(=O)[C@@H]1CN(C)C(=O)CN1C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 5, 1, 11, 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] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 23, 10, 10, 10, 10, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 23, 23, 23, 10, 10, 10, 10, 10, 10, 10, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878945 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001439878945 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878945/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878945/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001439878945 Building ZINC001445165516 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445165516' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445165516 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001445165516 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445165516/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445165516 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/412 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(=O)n(C)cc1NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001445165516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001445165516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445165516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001445165516 none Cc1cc(=O)n(C)cc1NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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, 11, 8, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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: [12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 19, 19, 19, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 4, 5, 19, 19, 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, 39]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445165516 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445165516/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445165516 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 413) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/413 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/413' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(=O)n(C)cc1NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001445165516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001445165516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445165516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001445165516 none Cc1cc(=O)n(C)cc1NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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, 11, 8, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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: [13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 19, 19, 19, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 4, 5, 19, 19, 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, 39]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445165516 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001445165516 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445165516/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445165516/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445165516 Building ZINC001445165516 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445165516' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445165516 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001445165516 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445165516/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445165516 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 412) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/412: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(=O)n(C)cc1NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001445165516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001445165516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445165516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001445165516 none Cc1cc(=O)n(C)cc1NC(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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, 11, 8, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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: [12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 19, 19, 19, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 4, 5, 19, 19, 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, 39]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445165516 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445165516/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445165516 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 413) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/413: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(=O)n(C)cc1NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001445165516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001445165516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445165516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001445165516 none Cc1cc(=O)n(C)cc1NC(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', '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, 11, 8, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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: [13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 19, 19, 19, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 4, 5, 19, 19, 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, 39]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445165516 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001445165516 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445165516/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445165516/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445165516 Building ZINC001445549537 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445549537' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445549537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001445549537 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445549537/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445549537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/414 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c(=O)n(C)c1) `ZINC001445549537.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001445549537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445549537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001445549537 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c(=O)n(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 11, 8, 5, 1, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 5, 1, 1, 1, 5, 5, 5, 18, 18, 18, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 18, 18, 5, 5, 5, 5, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445549537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445549537/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445549537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 415) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/415 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/415' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c(=O)n(C)c1) `ZINC001445549537.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001445549537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445549537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001445549537 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c(=O)n(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 11, 8, 5, 1, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 5, 1, 1, 1, 5, 5, 5, 18, 18, 18, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 18, 18, 5, 5, 5, 5, 13, 13, 13, 13] 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445549537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001445549537 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445549537/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445549537/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445549537 Building ZINC001445549537 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445549537' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445549537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001445549537 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445549537/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445549537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 414) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/414: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c(=O)n(C)c1) `ZINC001445549537.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001445549537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445549537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001445549537 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c(=O)n(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 11, 8, 5, 1, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 5, 1, 1, 1, 5, 5, 5, 18, 18, 18, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 18, 18, 5, 5, 5, 5, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445549537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445549537/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445549537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 415) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/415: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c(=O)n(C)c1) `ZINC001445549537.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001445549537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445549537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001445549537 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)c(=O)n(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 1, 11, 8, 5, 1, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 5, 1, 1, 1, 5, 5, 5, 18, 18, 18, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 18, 18, 5, 5, 5, 5, 13, 13, 13, 13] 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445549537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001445549537 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445549537/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445549537/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001445549537 Building ZINC001447208655 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208655' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208655 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001447208655 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208655/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208655 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/416 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001447208655.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001447208655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001447208655 none Cn1cnnc1[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', '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', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 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, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 7, 7, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 4, 4, 4, 12, 12, 12, 4, 4, 4, 10, 10, 10, 10, 7, 7, 7, 7, 7, 7, 4, 12, 12, 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: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208655 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208655/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208655 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 417) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/417 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/417' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001447208655.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001447208655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001447208655 none Cn1cnnc1[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', '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', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 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, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 13, 13, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 4, 4, 18, 18, 18, 18, 13, 13, 13, 13, 13, 13, 4, 13, 13, 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: 75 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208655 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001447208655 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208655/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208655/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208655 Building ZINC001447208655 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208655' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208655 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001447208655 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208655/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208655 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 416) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/416: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001447208655.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001447208655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001447208655 none Cn1cnnc1[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', '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', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 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, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 7, 7, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 4, 4, 4, 12, 12, 12, 4, 4, 4, 10, 10, 10, 10, 7, 7, 7, 7, 7, 7, 4, 12, 12, 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: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208655 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208655/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208655 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 417) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/417: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001447208655.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001447208655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001447208655 none Cn1cnnc1[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', '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', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 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, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 13, 13, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 4, 4, 18, 18, 18, 18, 13, 13, 13, 13, 13, 13, 4, 13, 13, 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: 75 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208655 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001447208655 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208655/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208655/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208655 Building ZINC001447208659 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208659' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208659 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001447208659 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208659/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208659 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/418 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001447208659.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001447208659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001447208659 none Cn1cnnc1[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', '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', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 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, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 13, 13, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 4, 4, 4, 12, 12, 12, 4, 4, 4, 19, 19, 19, 19, 13, 13, 13, 13, 13, 13, 4, 12, 12, 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: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208659 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208659/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208659 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 419) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/419 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/419' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001447208659.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001447208659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001447208659 none Cn1cnnc1[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', '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', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 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, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 7, 7, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 4, 4, 11, 11, 11, 11, 7, 7, 7, 7, 7, 7, 4, 13, 13, 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: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208659 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001447208659 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208659/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208659/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208659 Building ZINC001447208659 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208659' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208659 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001447208659 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208659/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208659 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 418) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/418: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001447208659.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001447208659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001447208659 none Cn1cnnc1[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', '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', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 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, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 13, 13, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 4, 4, 4, 12, 12, 12, 4, 4, 4, 19, 19, 19, 19, 13, 13, 13, 13, 13, 13, 4, 12, 12, 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: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208659 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208659/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208659 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 419) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/419: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001447208659.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001447208659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001447208659 none Cn1cnnc1[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', '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', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 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, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 7, 7, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 4, 4, 11, 11, 11, 11, 7, 7, 7, 7, 7, 7, 4, 13, 13, 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: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208659 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001447208659 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208659/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208659/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447208659 Building ZINC001447794909 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447794909' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447794909 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001447794909 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447794909/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447794909 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/420 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cnc(O)nc2N)CC1) `ZINC001447794909.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001447794909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447794909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001447794909 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cnc(O)nc2N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 8, 1, 12, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 6, 11, 19, 19, 19, 19, 37, 37, 27, 37, 37, 37, 37, 19, 19, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 37, 74, 37, 37, 19, 19, 19, 19] 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, 43, 44, 45, 46]) total number of confs: 188 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447794909 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447794909/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447794909 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 421) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/421 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/421' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cnc(O)nc2N)CC1) `ZINC001447794909.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001447794909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447794909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001447794909 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cnc(O)nc2N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 8, 1, 12, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 6, 12, 19, 19, 19, 19, 36, 36, 26, 36, 36, 36, 36, 19, 19, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 36, 72, 36, 36, 19, 19, 19, 19] 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, 43, 44, 45, 46]) total number of confs: 184 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447794909 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001447794909 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447794909/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447794909/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447794909 Building ZINC001447794909 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447794909' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447794909 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001447794909 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447794909/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447794909 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 420) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/420: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cnc(O)nc2N)CC1) `ZINC001447794909.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001447794909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447794909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001447794909 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(c2cnc(O)nc2N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 8, 1, 12, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 6, 11, 19, 19, 19, 19, 37, 37, 27, 37, 37, 37, 37, 19, 19, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 37, 74, 37, 37, 19, 19, 19, 19] 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, 43, 44, 45, 46]) total number of confs: 188 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447794909 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447794909/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447794909 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 421) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/421: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cnc(O)nc2N)CC1) `ZINC001447794909.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001447794909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447794909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001447794909 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(c2cnc(O)nc2N)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 8, 1, 12, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 6, 12, 19, 19, 19, 19, 36, 36, 26, 36, 36, 36, 36, 19, 19, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 36, 72, 36, 36, 19, 19, 19, 19] 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, 43, 44, 45, 46]) total number of confs: 184 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447794909 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001447794909 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447794909/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447794909/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001447794909 Building ZINC001449763587 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763587' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763587 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449763587 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763587/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763587 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/422 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1([S@](C)=O)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC001449763587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449763587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001449763587 none CCOC(=O)C1([S@](C)=O)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.o', 'C.3', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 14, 5, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 28, 28, 8, 28, 8, 8, 16, 16, 8, 8, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 33, 33, 33, 33, 33, 16, 16, 16, 8, 8, 8, 8, 2, 2, 2, 2, 2, 8, 8, 8, 8] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763587 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763587/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763587 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 423) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/423 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/423' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1([S@](C)=O)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC001449763587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449763587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001449763587 none CCOC(=O)C1([S@](C)=O)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.o', 'C.3', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 14, 5, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 8, 26, 8, 8, 12, 12, 8, 8, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 32, 32, 32, 32, 32, 12, 12, 12, 8, 8, 8, 8, 2, 2, 2, 2, 2, 8, 8, 8, 8] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763587 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001449763587 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763587/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763587/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763587 Building ZINC001449763587 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763587' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763587 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449763587 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763587/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763587 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 422) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/422: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1([S@](C)=O)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC001449763587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449763587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001449763587 none CCOC(=O)C1([S@](C)=O)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.o', 'C.3', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 14, 5, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 28, 28, 8, 28, 8, 8, 16, 16, 8, 8, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 33, 33, 33, 33, 33, 16, 16, 16, 8, 8, 8, 8, 2, 2, 2, 2, 2, 8, 8, 8, 8] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763587 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763587/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763587 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 423) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/423: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1([S@](C)=O)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC001449763587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449763587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001449763587 none CCOC(=O)C1([S@](C)=O)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.o', 'C.3', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 14, 5, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 8, 26, 8, 8, 12, 12, 8, 8, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 32, 32, 32, 32, 32, 12, 12, 12, 8, 8, 8, 8, 2, 2, 2, 2, 2, 8, 8, 8, 8] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763587 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001449763587 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763587/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763587/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763587 Building ZINC001449763589 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763589' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763589 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449763589 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763589/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763589 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/424 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1([S@@](C)=O)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC001449763589.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449763589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001449763589 none CCOC(=O)C1([S@@](C)=O)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.o', 'C.3', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 14, 5, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 8, 31, 8, 8, 14, 14, 8, 8, 5, 2, 5, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 32, 32, 32, 32, 32, 14, 14, 14, 8, 8, 8, 8, 3, 3, 3, 3, 3, 8, 8, 8, 8] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763589 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763589/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763589 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 425) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/425 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/425' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1([S@@](C)=O)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC001449763589.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449763589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763589/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001449763589 none CCOC(=O)C1([S@@](C)=O)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.o', 'C.3', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 14, 5, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 27, 27, 8, 27, 8, 8, 14, 14, 8, 8, 5, 2, 5, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 30, 30, 30, 30, 30, 14, 14, 14, 8, 8, 8, 8, 3, 3, 3, 3, 3, 8, 8, 8, 8] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763589 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001449763589 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763589/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763589/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763589 Building ZINC001449763589 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763589' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763589 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449763589 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763589/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763589 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 424) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/424: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1([S@@](C)=O)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC001449763589.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449763589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001449763589 none CCOC(=O)C1([S@@](C)=O)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.o', 'C.3', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 14, 5, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 8, 31, 8, 8, 14, 14, 8, 8, 5, 2, 5, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 32, 32, 32, 32, 32, 14, 14, 14, 8, 8, 8, 8, 3, 3, 3, 3, 3, 8, 8, 8, 8] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763589 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763589/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763589 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 425) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/425: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1([S@@](C)=O)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC001449763589.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449763589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763589/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001449763589 none CCOC(=O)C1([S@@](C)=O)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'S.o', 'C.3', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 14, 5, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 27, 27, 8, 27, 8, 8, 14, 14, 8, 8, 5, 2, 5, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 30, 30, 30, 30, 30, 14, 14, 14, 8, 8, 8, 8, 3, 3, 3, 3, 3, 8, 8, 8, 8] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763589 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001449763589 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763589/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763589/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001449763589 Building ZINC001451794927 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794927' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794927 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451794927 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794927/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794927 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/426 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n1) `ZINC001451794927.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451794927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001451794927 none Cc1ccnc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.ar', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 6, 6, 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: [21, 21, 5, 21, 21, 5, 3, 5, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 8, 8, 8, 4, 4, 4, 21, 21, 21, 21, 5, 21, 5, 5, 5, 3, 4, 8, 8, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794927 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794927/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794927 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 427) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/427 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/427' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n1) `ZINC001451794927.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451794927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001451794927 none Cc1ccnc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.ar', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 6, 6, 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: [23, 23, 5, 23, 23, 5, 3, 5, 5, 3, 1, 3, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 23, 23, 23, 23, 5, 23, 5, 5, 5, 3, 3, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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/323031/xbw-8058115.49/working/building/ZINC001451794927 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001451794927 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794927/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794927/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794927 Building ZINC001451794927 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794927' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794927 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451794927 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794927/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794927 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 426) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/426: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n1) `ZINC001451794927.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451794927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001451794927 none Cc1ccnc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.ar', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 6, 6, 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: [21, 21, 5, 21, 21, 5, 3, 5, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 8, 8, 8, 4, 4, 4, 21, 21, 21, 21, 5, 21, 5, 5, 5, 3, 4, 8, 8, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794927 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794927/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794927 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 427) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/427: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n1) `ZINC001451794927.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451794927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001451794927 none Cc1ccnc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.ar', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 6, 6, 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: [23, 23, 5, 23, 23, 5, 3, 5, 5, 3, 1, 3, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 23, 23, 23, 23, 5, 23, 5, 5, 5, 3, 3, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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/323031/xbw-8058115.49/working/building/ZINC001451794927 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001451794927 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794927/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794927/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794927 Building ZINC001451794932 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794932' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794932 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451794932 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794932/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794932 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/428 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n1) `ZINC001451794932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451794932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001451794932 none Cc1ccnc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.ar', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 6, 6, 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: [23, 23, 5, 23, 23, 5, 3, 5, 5, 3, 1, 3, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 23, 23, 23, 23, 5, 23, 5, 5, 5, 3, 3, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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/323031/xbw-8058115.49/working/building/ZINC001451794932 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794932/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794932 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 429) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/429 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/429' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n1) `ZINC001451794932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451794932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001451794932 none Cc1ccnc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.ar', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 6, 6, 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: [22, 22, 5, 22, 22, 5, 3, 5, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 8, 8, 8, 4, 4, 4, 22, 22, 22, 22, 8, 22, 5, 5, 5, 3, 4, 8, 8, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794932 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001451794932 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794932/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794932/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794932 Building ZINC001451794932 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794932' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794932 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451794932 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794932/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794932 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 428) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/428: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n1) `ZINC001451794932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451794932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001451794932 none Cc1ccnc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.ar', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 6, 6, 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: [23, 23, 5, 23, 23, 5, 3, 5, 5, 3, 1, 3, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 23, 23, 23, 23, 5, 23, 5, 5, 5, 3, 3, 6, 6, 3, 3, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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/323031/xbw-8058115.49/working/building/ZINC001451794932 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794932/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794932 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 429) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/429: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n1) `ZINC001451794932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451794932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001451794932 none Cc1ccnc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'N.ar', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 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, 4, 6, 6, 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: [22, 22, 5, 22, 22, 5, 3, 5, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 8, 8, 8, 4, 4, 4, 22, 22, 22, 22, 8, 22, 5, 5, 5, 3, 4, 8, 8, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794932 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001451794932 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794932/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794932/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001451794932 Building ZINC001454960713 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001454960713' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001454960713 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454960713 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001454960713/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001454960713 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/430 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(CN3C(=O)CNC3=O)cc2)cn1) `ZINC001454960713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454960713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001454960713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001454960713 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(CN3C(=O)CNC3=O)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 10, 14, 14, 14, 14, 24, 46, 46, 46, 46, 46, 46, 14, 14, 4, 4, 4, 4, 4, 4, 2, 10, 10, 14, 14, 24, 24, 46, 46, 46, 14, 14, 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]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001454960713 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001454960713/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001454960713 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 431) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/431 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/431' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(CN3C(=O)CNC3=O)cc2)cn1) `ZINC001454960713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454960713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001454960713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001454960713 none Cn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(CN3C(=O)CNC3=O)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 10, 14, 14, 10, 12, 24, 46, 46, 46, 46, 46, 46, 14, 14, 4, 4, 4, 4, 4, 4, 2, 10, 10, 14, 14, 24, 24, 46, 46, 46, 14, 14, 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]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001454960713 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001454960713 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001454960713/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001454960713/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001454960713 Building ZINC001454960713 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001454960713' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001454960713 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454960713 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001454960713/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001454960713 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 430) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/430: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(CN3C(=O)CNC3=O)cc2)cn1) `ZINC001454960713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454960713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001454960713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001454960713 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(CN3C(=O)CNC3=O)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 10, 14, 14, 14, 14, 24, 46, 46, 46, 46, 46, 46, 14, 14, 4, 4, 4, 4, 4, 4, 2, 10, 10, 14, 14, 24, 24, 46, 46, 46, 14, 14, 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]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001454960713 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001454960713/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001454960713 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 431) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/431: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(CN3C(=O)CNC3=O)cc2)cn1) `ZINC001454960713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454960713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001454960713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001454960713 none Cn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(CN3C(=O)CNC3=O)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 10, 14, 14, 10, 12, 24, 46, 46, 46, 46, 46, 46, 14, 14, 4, 4, 4, 4, 4, 4, 2, 10, 10, 14, 14, 24, 24, 46, 46, 46, 14, 14, 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]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001454960713 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001454960713 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001454960713/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001454960713/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001454960713 Building ZINC001455050634 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050634' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050634 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455050634 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050634/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050634 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/432 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC(C)(C)[C@H](O)C(F)(F)F) `ZINC001455050634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455050634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001455050634 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC(C)(C)[C@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 14, 4, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 14, 14, 4, 3, 9, 9, 9, 9, 9, 9, 45] 150 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]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050634 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050634/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050634 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 433) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/433 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/433' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC(C)(C)[C@H](O)C(F)(F)F) `ZINC001455050634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455050634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001455050634 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC(C)(C)[C@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 11, 11, 11, 4, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4, 11, 11, 4, 4, 10, 10, 10, 10, 10, 10, 54] 150 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]) total number of confs: 166 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050634 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001455050634 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050634/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050634/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050634 Building ZINC001455050634 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050634' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050634 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455050634 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050634/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050634 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 432) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/432: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC(C)(C)[C@H](O)C(F)(F)F) `ZINC001455050634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455050634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001455050634 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC(C)(C)[C@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 14, 4, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 14, 14, 4, 3, 9, 9, 9, 9, 9, 9, 45] 150 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]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050634 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050634/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050634 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 433) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/433: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC(C)(C)[C@H](O)C(F)(F)F) `ZINC001455050634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455050634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001455050634 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC(C)(C)[C@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 11, 11, 11, 4, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4, 11, 11, 4, 4, 10, 10, 10, 10, 10, 10, 54] 150 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]) total number of confs: 166 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050634 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001455050634 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050634/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050634/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050634 Building ZINC001455050639 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050639' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050639 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455050639 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050639/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050639 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/434 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC(C)(C)[C@@H](O)C(F)(F)F) `ZINC001455050639.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455050639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001455050639 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC(C)(C)[C@@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 11, 11, 11, 4, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4, 11, 11, 4, 4, 10, 10, 10, 10, 10, 10, 54] 150 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]) total number of confs: 166 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050639 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050639/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050639 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 435) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/435 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/435' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC(C)(C)[C@@H](O)C(F)(F)F) `ZINC001455050639.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455050639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050639/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001455050639 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC(C)(C)[C@@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 13, 4, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 13, 13, 4, 4, 10, 10, 10, 10, 10, 10, 57] 150 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]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050639 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001455050639 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050639/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050639/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050639 Building ZINC001455050639 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050639' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050639 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455050639 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050639/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050639 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 434) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/434: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC(C)(C)[C@@H](O)C(F)(F)F) `ZINC001455050639.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455050639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001455050639 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC(C)(C)[C@@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 11, 11, 11, 4, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4, 11, 11, 4, 4, 10, 10, 10, 10, 10, 10, 54] 150 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]) total number of confs: 166 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050639 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050639/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050639 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 435) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/435: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC(C)(C)[C@@H](O)C(F)(F)F) `ZINC001455050639.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455050639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050639/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001455050639 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC(C)(C)[C@@H](O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 12, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 13, 4, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 13, 13, 4, 4, 10, 10, 10, 10, 10, 10, 57] 150 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]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050639 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001455050639 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050639/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050639/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455050639 Building ZINC001455450704 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450704' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450704 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455450704 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450704/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450704 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/436 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCCC[C@@H]1CCOC1=O) `ZINC001455450704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455450704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001455450704 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCCC[C@@H]1CCOC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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.3', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 12, 1, 11, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 13, 18, 25, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 4, 4, 1, 3, 13, 13, 18, 18, 19, 19, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 25, 26, 27, 28, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 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/323031/xbw-8058115.49/working/building/ZINC001455450704 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450704/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450704 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 437) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/437 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/437' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCCC[C@@H]1CCOC1=O) `ZINC001455450704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455450704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001455450704 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCCC[C@@H]1CCOC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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.3', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 12, 1, 11, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 2, 2, 2, 12, 14, 20, 23, 23, 23, 23, 23, 23, 2, 2, 2, 2, 5, 5, 2, 2, 12, 12, 15, 15, 16, 16, 23, 23, 23, 23] 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, 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/323031/xbw-8058115.49/working/building/ZINC001455450704 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001455450704 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450704/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450704/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450704 Building ZINC001455450704 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450704' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450704 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455450704 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450704/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450704 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 436) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/436: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCCC[C@@H]1CCOC1=O) `ZINC001455450704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455450704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001455450704 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCCC[C@@H]1CCOC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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.3', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 12, 1, 11, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 13, 18, 25, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 4, 4, 1, 3, 13, 13, 18, 18, 19, 19, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 25, 26, 27, 28, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 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/323031/xbw-8058115.49/working/building/ZINC001455450704 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450704/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450704 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 437) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/437: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCCC[C@@H]1CCOC1=O) `ZINC001455450704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455450704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001455450704 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCCC[C@@H]1CCOC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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.3', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 12, 1, 11, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 2, 2, 2, 12, 14, 20, 23, 23, 23, 23, 23, 23, 2, 2, 2, 2, 5, 5, 2, 2, 12, 12, 15, 15, 16, 16, 23, 23, 23, 23] 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, 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/323031/xbw-8058115.49/working/building/ZINC001455450704 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001455450704 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450704/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450704/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450704 Building ZINC001455450706 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450706' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450706 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455450706 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450706/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450706 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/438 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCCC[C@H]1CCOC1=O) `ZINC001455450706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455450706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001455450706 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCCC[C@H]1CCOC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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.3', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 12, 1, 11, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 2, 2, 2, 12, 14, 20, 23, 23, 23, 23, 23, 23, 2, 2, 2, 2, 5, 5, 2, 2, 12, 12, 15, 15, 16, 16, 23, 23, 23, 23] 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, 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/323031/xbw-8058115.49/working/building/ZINC001455450706 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450706/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450706 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 439) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/439 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/439' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCCC[C@H]1CCOC1=O) `ZINC001455450706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455450706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001455450706 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCCC[C@H]1CCOC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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.3', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 12, 1, 11, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 13, 18, 25, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 4, 4, 1, 3, 13, 13, 18, 18, 19, 19, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 25, 26, 27, 28, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 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/323031/xbw-8058115.49/working/building/ZINC001455450706 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001455450706 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450706/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450706/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450706 Building ZINC001455450706 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450706' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450706 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455450706 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450706/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450706 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 438) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/438: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCCC[C@H]1CCOC1=O) `ZINC001455450706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455450706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001455450706 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCCC[C@H]1CCOC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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.3', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 12, 1, 11, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 2, 2, 2, 12, 14, 20, 23, 23, 23, 23, 23, 23, 2, 2, 2, 2, 5, 5, 2, 2, 12, 12, 15, 15, 16, 16, 23, 23, 23, 23] 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, 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/323031/xbw-8058115.49/working/building/ZINC001455450706 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450706/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450706 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 439) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/439: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCCC[C@H]1CCOC1=O) `ZINC001455450706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455450706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001455450706 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCCC[C@H]1CCOC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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.3', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 12, 1, 11, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 13, 18, 25, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 4, 4, 1, 3, 13, 13, 18, 18, 19, 19, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 25, 26, 27, 28, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 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/323031/xbw-8058115.49/working/building/ZINC001455450706 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001455450706 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450706/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450706/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455450706 Building ZINC001455529140 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001455529140 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/440 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455529140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529140 none CCOC1CC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 2, 13, 2, 1, 2, 1, 1, 1, 3, 3, 3, 7, 7, 7, 3, 3, 3, 17, 21, 21, 21, 21, 21, 17, 17, 17, 17, 17, 2, 3, 7, 7, 3, 3, 3, 3, 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 441) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/441 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/441' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455529140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529140 none CCOC1CC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 2, 13, 2, 1, 2, 1, 1, 1, 3, 3, 3, 7, 7, 7, 3, 3, 3, 17, 21, 21, 21, 21, 21, 17, 17, 17, 17, 17, 2, 3, 7, 7, 3, 3, 3, 3, 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 442) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/442 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/442' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529140.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001455529140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529140 none CCOC1CC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 2, 15, 2, 1, 2, 1, 1, 1, 4, 4, 4, 7, 7, 7, 4, 4, 4, 17, 20, 20, 20, 20, 20, 17, 17, 17, 17, 17, 2, 4, 7, 7, 4, 4, 4, 4, 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 443) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/443 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/443' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529140.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001455529140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529140 none CCOC1CC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 2, 15, 2, 1, 2, 1, 1, 1, 4, 4, 4, 7, 7, 7, 4, 4, 4, 17, 20, 20, 20, 20, 20, 17, 17, 17, 17, 17, 2, 4, 7, 7, 4, 4, 4, 4, 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001455529140 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 Building ZINC001455529140 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001455529140 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 440) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/440: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455529140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529140 none CCOC1CC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 2, 13, 2, 1, 2, 1, 1, 1, 3, 3, 3, 7, 7, 7, 3, 3, 3, 17, 21, 21, 21, 21, 21, 17, 17, 17, 17, 17, 2, 3, 7, 7, 3, 3, 3, 3, 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 441) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/441: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455529140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529140 none CCOC1CC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 2, 13, 2, 1, 2, 1, 1, 1, 3, 3, 3, 7, 7, 7, 3, 3, 3, 17, 21, 21, 21, 21, 21, 17, 17, 17, 17, 17, 2, 3, 7, 7, 3, 3, 3, 3, 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 442) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/442: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529140.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001455529140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529140 none CCOC1CC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 2, 15, 2, 1, 2, 1, 1, 1, 4, 4, 4, 7, 7, 7, 4, 4, 4, 17, 20, 20, 20, 20, 20, 17, 17, 17, 17, 17, 2, 4, 7, 7, 4, 4, 4, 4, 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 443) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/443: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529140.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001455529140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529140 none CCOC1CC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 2, 15, 2, 1, 2, 1, 1, 1, 4, 4, 4, 7, 7, 7, 4, 4, 4, 17, 20, 20, 20, 20, 20, 17, 17, 17, 17, 17, 2, 4, 7, 7, 4, 4, 4, 4, 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001455529140 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 Building ZINC001455529140 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001455529140 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 440) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/440: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455529140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529140 none CCOC1CC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 2, 13, 2, 1, 2, 1, 1, 1, 3, 3, 3, 7, 7, 7, 3, 3, 3, 17, 21, 21, 21, 21, 21, 17, 17, 17, 17, 17, 2, 3, 7, 7, 3, 3, 3, 3, 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 441) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/441: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455529140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529140 none CCOC1CC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 2, 13, 2, 1, 2, 1, 1, 1, 3, 3, 3, 7, 7, 7, 3, 3, 3, 17, 21, 21, 21, 21, 21, 17, 17, 17, 17, 17, 2, 3, 7, 7, 3, 3, 3, 3, 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 442) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/442: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529140.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001455529140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529140 none CCOC1CC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 2, 15, 2, 1, 2, 1, 1, 1, 4, 4, 4, 7, 7, 7, 4, 4, 4, 17, 20, 20, 20, 20, 20, 17, 17, 17, 17, 17, 2, 4, 7, 7, 4, 4, 4, 4, 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 443) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/443: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529140.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001455529140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529140 none CCOC1CC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 2, 15, 2, 1, 2, 1, 1, 1, 4, 4, 4, 7, 7, 7, 4, 4, 4, 17, 20, 20, 20, 20, 20, 17, 17, 17, 17, 17, 2, 4, 7, 7, 4, 4, 4, 4, 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001455529140 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 Building ZINC001455529140 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001455529140 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 440) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/440: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455529140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529140 none CCOC1CC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 2, 13, 2, 1, 2, 1, 1, 1, 3, 3, 3, 7, 7, 7, 3, 3, 3, 17, 21, 21, 21, 21, 21, 17, 17, 17, 17, 17, 2, 3, 7, 7, 3, 3, 3, 3, 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 441) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/441: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455529140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529140 none CCOC1CC2(C[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 2, 13, 2, 1, 2, 1, 1, 1, 3, 3, 3, 7, 7, 7, 3, 3, 3, 17, 21, 21, 21, 21, 21, 17, 17, 17, 17, 17, 2, 3, 7, 7, 3, 3, 3, 3, 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 442) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/442: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529140.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001455529140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529140 none CCOC1CC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 2, 15, 2, 1, 2, 1, 1, 1, 4, 4, 4, 7, 7, 7, 4, 4, 4, 17, 20, 20, 20, 20, 20, 17, 17, 17, 17, 17, 2, 4, 7, 7, 4, 4, 4, 4, 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 443) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/443: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529140.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001455529140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529140 none CCOC1CC2(C[C@@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 2, 15, 2, 1, 2, 1, 1, 1, 4, 4, 4, 7, 7, 7, 4, 4, 4, 17, 20, 20, 20, 20, 20, 17, 17, 17, 17, 17, 2, 4, 7, 7, 4, 4, 4, 4, 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001455529140 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529140 Building ZINC001455529141 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001455529141 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/444 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455529141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529141 none CCOC1CC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 16, 3, 16, 3, 1, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 16, 24, 24, 24, 24, 24, 16, 16, 16, 16, 16, 3, 2, 5, 5, 2, 2, 2, 2, 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 445) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/445 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/445' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455529141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529141 none CCOC1CC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 16, 3, 16, 3, 1, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 16, 24, 24, 24, 24, 24, 16, 16, 16, 16, 16, 3, 2, 5, 5, 2, 2, 2, 2, 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 446) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/446 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/446' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529141.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001455529141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529141 none CCOC1CC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 24, 14, 14, 14, 14, 14, 2, 14, 2, 1, 2, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 14, 25, 25, 25, 25, 25, 14, 14, 14, 14, 14, 2, 3, 6, 6, 3, 3, 3, 3, 14, 14] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 447) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/447 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/447' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529141.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001455529141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529141 none CCOC1CC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 24, 14, 14, 14, 14, 14, 2, 14, 2, 1, 2, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 14, 25, 25, 25, 25, 25, 14, 14, 14, 14, 14, 2, 3, 6, 6, 3, 3, 3, 3, 14, 14] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001455529141 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 Building ZINC001455529141 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001455529141 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 444) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/444: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455529141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529141 none CCOC1CC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 16, 3, 16, 3, 1, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 16, 24, 24, 24, 24, 24, 16, 16, 16, 16, 16, 3, 2, 5, 5, 2, 2, 2, 2, 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 445) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/445: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455529141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529141 none CCOC1CC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 16, 3, 16, 3, 1, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 16, 24, 24, 24, 24, 24, 16, 16, 16, 16, 16, 3, 2, 5, 5, 2, 2, 2, 2, 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 446) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/446: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529141.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001455529141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529141 none CCOC1CC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 24, 14, 14, 14, 14, 14, 2, 14, 2, 1, 2, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 14, 25, 25, 25, 25, 25, 14, 14, 14, 14, 14, 2, 3, 6, 6, 3, 3, 3, 3, 14, 14] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 447) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/447: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529141.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001455529141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529141 none CCOC1CC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 24, 14, 14, 14, 14, 14, 2, 14, 2, 1, 2, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 14, 25, 25, 25, 25, 25, 14, 14, 14, 14, 14, 2, 3, 6, 6, 3, 3, 3, 3, 14, 14] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001455529141 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 Building ZINC001455529141 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001455529141 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 444) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/444: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455529141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529141 none CCOC1CC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 16, 3, 16, 3, 1, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 16, 24, 24, 24, 24, 24, 16, 16, 16, 16, 16, 3, 2, 5, 5, 2, 2, 2, 2, 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 445) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/445: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455529141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529141 none CCOC1CC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 16, 3, 16, 3, 1, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 16, 24, 24, 24, 24, 24, 16, 16, 16, 16, 16, 3, 2, 5, 5, 2, 2, 2, 2, 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 446) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/446: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529141.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001455529141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529141 none CCOC1CC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 24, 14, 14, 14, 14, 14, 2, 14, 2, 1, 2, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 14, 25, 25, 25, 25, 25, 14, 14, 14, 14, 14, 2, 3, 6, 6, 3, 3, 3, 3, 14, 14] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 447) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/447: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529141.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001455529141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529141 none CCOC1CC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 24, 14, 14, 14, 14, 14, 2, 14, 2, 1, 2, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 14, 25, 25, 25, 25, 25, 14, 14, 14, 14, 14, 2, 3, 6, 6, 3, 3, 3, 3, 14, 14] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001455529141 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 Building ZINC001455529141 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001455529141 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 444) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/444: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455529141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529141 none CCOC1CC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 16, 3, 16, 3, 1, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 16, 24, 24, 24, 24, 24, 16, 16, 16, 16, 16, 3, 2, 5, 5, 2, 2, 2, 2, 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 445) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/445: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455529141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529141 none CCOC1CC2(C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 16, 3, 16, 3, 1, 3, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 16, 24, 24, 24, 24, 24, 16, 16, 16, 16, 16, 3, 2, 5, 5, 2, 2, 2, 2, 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 446) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/446: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529141.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001455529141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529141 none CCOC1CC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 24, 14, 14, 14, 14, 14, 2, 14, 2, 1, 2, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 14, 25, 25, 25, 25, 25, 14, 14, 14, 14, 14, 2, 3, 6, 6, 3, 3, 3, 3, 14, 14] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 447) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/447: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455529141.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001455529141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001455529141 none CCOC1CC2(C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 24, 14, 14, 14, 14, 14, 2, 14, 2, 1, 2, 1, 1, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 14, 25, 25, 25, 25, 25, 14, 14, 14, 14, 14, 2, 3, 6, 6, 3, 3, 3, 3, 14, 14] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001455529141 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455529141 Building ZINC001455680212 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680212' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680212 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455680212 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680212/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680212 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/448 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1Cc2n[nH]cc2CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455680212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455680212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001455680212 none C[C@@H]1Cc2n[nH]cc2CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', '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, 5, 1, 8, 8, 6, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 1, 8, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 8, 8, 2, 2, 2, 2, 11, 11] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 50 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680212 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680212/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680212 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 449) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/449 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/449' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1Cc2n[nH]cc2CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455680212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455680212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001455680212 none C[C@@H]1Cc2n[nH]cc2CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', '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, 5, 1, 8, 8, 6, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 1, 9, 1, 1, 1, 3, 3, 3, 12, 12, 12, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 12, 12, 3, 3, 3, 3, 11, 11] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 62 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680212 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001455680212 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680212/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680212/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680212 Building ZINC001455680212 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680212' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680212 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455680212 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680212/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680212 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 448) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/448: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1Cc2n[nH]cc2CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455680212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455680212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001455680212 none C[C@@H]1Cc2n[nH]cc2CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', '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, 5, 1, 8, 8, 6, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 1, 8, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 8, 8, 2, 2, 2, 2, 11, 11] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 50 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680212 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680212/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680212 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 449) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/449: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1Cc2n[nH]cc2CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455680212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455680212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001455680212 none C[C@@H]1Cc2n[nH]cc2CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', '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, 5, 1, 8, 8, 6, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 1, 9, 1, 1, 1, 3, 3, 3, 12, 12, 12, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 12, 12, 3, 3, 3, 3, 11, 11] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 62 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680212 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001455680212 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680212/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680212/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680212 Building ZINC001455680214 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680214' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680214 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455680214 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680214/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680214 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/450 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1Cc2n[nH]cc2CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455680214.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455680214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001455680214 none C[C@H]1Cc2n[nH]cc2CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', '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, 5, 1, 8, 8, 6, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 1, 9, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 8, 8, 2, 2, 2, 2, 10, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680214 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680214/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680214 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 451) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/451 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/451' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1Cc2n[nH]cc2CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455680214.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455680214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680214/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001455680214 none C[C@H]1Cc2n[nH]cc2CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', '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, 5, 1, 8, 8, 6, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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: [13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 1, 10, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 8, 8, 2, 2, 2, 2, 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680214 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001455680214 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680214/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680214/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680214 Building ZINC001455680214 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680214' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680214 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455680214 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680214/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680214 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 450) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/450: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1Cc2n[nH]cc2CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455680214.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455680214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001455680214 none C[C@H]1Cc2n[nH]cc2CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', '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, 5, 1, 8, 8, 6, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 1, 9, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 8, 8, 2, 2, 2, 2, 10, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680214 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680214/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680214 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 451) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/451: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1Cc2n[nH]cc2CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001455680214.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455680214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680214/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001455680214 none C[C@H]1Cc2n[nH]cc2CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', '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, 5, 1, 8, 8, 6, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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: [13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 1, 10, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 8, 8, 2, 2, 2, 2, 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680214 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001455680214 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680214/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680214/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001455680214 Building ZINC001456509020 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509020' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509020 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456509020 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509020/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509020 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/452 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](C2CC2)O1) `ZINC001456509020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456509020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001456509020 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](C2CC2)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 17, 21, 21, 21, 21, 21, 21, 28, 28, 21, 1, 1, 1, 1, 4, 4, 1, 2, 14, 14, 21, 21, 21, 21, 28, 28, 28, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509020 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509020/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509020 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 453) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/453 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/453' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](C2CC2)O1) `ZINC001456509020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456509020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001456509020 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](C2CC2)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 18, 18, 18, 18, 18, 18, 24, 24, 18, 1, 1, 1, 1, 4, 4, 1, 2, 11, 11, 18, 18, 18, 18, 24, 24, 24, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509020 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001456509020 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509020/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509020/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509020 Building ZINC001456509020 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509020' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509020 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456509020 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509020/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509020 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 452) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/452: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](C2CC2)O1) `ZINC001456509020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456509020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001456509020 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](C2CC2)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 17, 21, 21, 21, 21, 21, 21, 28, 28, 21, 1, 1, 1, 1, 4, 4, 1, 2, 14, 14, 21, 21, 21, 21, 28, 28, 28, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509020 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509020/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509020 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 453) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/453: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](C2CC2)O1) `ZINC001456509020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456509020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001456509020 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@@H](C2CC2)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 12, 18, 18, 18, 18, 18, 18, 24, 24, 18, 1, 1, 1, 1, 4, 4, 1, 2, 11, 11, 18, 18, 18, 18, 24, 24, 24, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509020 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001456509020 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509020/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509020/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509020 Building ZINC001456509023 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509023' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509023 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456509023 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509023/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509023 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/454 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](C2CC2)O1) `ZINC001456509023.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456509023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001456509023 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](C2CC2)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 16, 24, 24, 24, 24, 24, 24, 28, 28, 24, 1, 1, 1, 1, 4, 4, 1, 3, 15, 15, 24, 24, 24, 24, 28, 28, 28, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509023 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509023/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509023 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 455) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/455 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/455' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](C2CC2)O1) `ZINC001456509023.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456509023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509023/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001456509023 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](C2CC2)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 2, 2, 2, 14, 25, 25, 25, 25, 25, 25, 27, 27, 25, 2, 2, 2, 2, 5, 5, 2, 2, 12, 12, 25, 25, 25, 25, 27, 27, 27, 27, 27] 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, 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/323031/xbw-8058115.49/working/building/ZINC001456509023 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001456509023 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509023/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509023/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509023 Building ZINC001456509023 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509023' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509023 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456509023 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509023/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509023 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 454) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/454: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](C2CC2)O1) `ZINC001456509023.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456509023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001456509023 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](C2CC2)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 16, 24, 24, 24, 24, 24, 24, 28, 28, 24, 1, 1, 1, 1, 4, 4, 1, 3, 15, 15, 24, 24, 24, 24, 28, 28, 28, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509023 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509023/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509023 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 455) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/455: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](C2CC2)O1) `ZINC001456509023.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456509023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509023/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001456509023 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CC[C@H](C2CC2)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 2, 2, 2, 14, 25, 25, 25, 25, 25, 25, 27, 27, 25, 2, 2, 2, 2, 5, 5, 2, 2, 12, 12, 25, 25, 25, 25, 27, 27, 27, 27, 27] 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, 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/323031/xbw-8058115.49/working/building/ZINC001456509023 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001456509023 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509023/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509023/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509023 Building ZINC001456509027 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509027' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509027 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456509027 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509027/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509027 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/456 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](C2CC2)O1) `ZINC001456509027.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456509027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001456509027 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](C2CC2)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 2, 2, 2, 17, 25, 25, 25, 25, 25, 25, 26, 26, 25, 2, 2, 2, 2, 5, 5, 2, 2, 14, 14, 25, 25, 25, 25, 26, 26, 26, 26, 26] 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, 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/323031/xbw-8058115.49/working/building/ZINC001456509027 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509027/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509027 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 457) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/457 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/457' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](C2CC2)O1) `ZINC001456509027.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456509027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001456509027 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](C2CC2)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 3, 3, 3, 16, 26, 26, 26, 26, 26, 26, 28, 28, 26, 2, 2, 2, 2, 5, 5, 2, 3, 15, 15, 26, 26, 26, 26, 28, 28, 28, 28, 28] 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, 42, 43, 44]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509027 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001456509027 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509027/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509027/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509027 Building ZINC001456509027 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509027' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509027 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456509027 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509027/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509027 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 456) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/456: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](C2CC2)O1) `ZINC001456509027.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456509027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001456509027 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](C2CC2)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 2, 2, 2, 17, 25, 25, 25, 25, 25, 25, 26, 26, 25, 2, 2, 2, 2, 5, 5, 2, 2, 14, 14, 25, 25, 25, 25, 26, 26, 26, 26, 26] 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, 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/323031/xbw-8058115.49/working/building/ZINC001456509027 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509027/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509027 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 457) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/457: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](C2CC2)O1) `ZINC001456509027.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456509027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001456509027 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@@H](C2CC2)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 3, 3, 3, 16, 26, 26, 26, 26, 26, 26, 28, 28, 26, 2, 2, 2, 2, 5, 5, 2, 3, 15, 15, 26, 26, 26, 26, 28, 28, 28, 28, 28] 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, 42, 43, 44]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509027 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001456509027 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509027/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509027/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509027 Building ZINC001456509031 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509031' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509031 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456509031 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509031/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509031 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/458 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](C2CC2)O1) `ZINC001456509031.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456509031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001456509031 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](C2CC2)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 14, 20, 20, 20, 20, 20, 20, 26, 26, 20, 1, 1, 1, 1, 4, 4, 1, 2, 12, 12, 20, 20, 20, 20, 26, 26, 26, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509031 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509031/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509031 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 459) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/459 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/459' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](C2CC2)O1) `ZINC001456509031.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456509031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509031/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001456509031 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](C2CC2)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 16, 20, 20, 20, 20, 20, 20, 27, 27, 20, 1, 1, 1, 1, 4, 4, 1, 2, 13, 13, 20, 20, 20, 20, 27, 27, 27, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509031 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001456509031 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509031/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509031/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509031 Building ZINC001456509031 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509031' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509031 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456509031 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509031/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509031 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 458) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/458: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](C2CC2)O1) `ZINC001456509031.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456509031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001456509031 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](C2CC2)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 14, 20, 20, 20, 20, 20, 20, 26, 26, 20, 1, 1, 1, 1, 4, 4, 1, 2, 12, 12, 20, 20, 20, 20, 26, 26, 26, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509031 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509031/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509031 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 459) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/459: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](C2CC2)O1) `ZINC001456509031.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456509031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509031/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001456509031 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CC[C@H](C2CC2)O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 16, 20, 20, 20, 20, 20, 20, 27, 27, 20, 1, 1, 1, 1, 4, 4, 1, 2, 13, 13, 20, 20, 20, 20, 27, 27, 27, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 32, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509031 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001456509031 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509031/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509031/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456509031 Building ZINC001456525239 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456525239' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456525239 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456525239 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456525239/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456525239 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/460 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCC[C@@H]1O) `ZINC001456525239.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456525239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456525239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001456525239 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCC[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 2, 2, 2, 13, 15, 22, 22, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 5, 5, 2, 2, 13, 13, 19, 19, 22, 22, 22, 22, 22, 22, 22, 22, 66] 150 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, 42, 43, 44, 45, 46]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456525239 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456525239/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456525239 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 461) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/461 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/461' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCC[C@@H]1O) `ZINC001456525239.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456525239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456525239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001456525239 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCC[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 2, 2, 2, 13, 15, 24, 24, 24, 24, 24, 24, 24, 24, 2, 2, 2, 2, 5, 5, 2, 2, 13, 13, 19, 19, 24, 24, 24, 24, 24, 24, 24, 24, 72] 150 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, 42, 43, 44, 45, 46]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456525239 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001456525239 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456525239/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456525239/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456525239 Building ZINC001456525239 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456525239' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456525239 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456525239 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456525239/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456525239 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 460) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/460: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCC[C@@H]1O) `ZINC001456525239.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456525239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456525239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001456525239 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCC[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 2, 2, 2, 13, 15, 22, 22, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 5, 5, 2, 2, 13, 13, 19, 19, 22, 22, 22, 22, 22, 22, 22, 22, 66] 150 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, 42, 43, 44, 45, 46]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456525239 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456525239/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456525239 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 461) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCC[C@@H]1O) `ZINC001456525239.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456525239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456525239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001456525239 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCC[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 2, 2, 2, 13, 15, 24, 24, 24, 24, 24, 24, 24, 24, 2, 2, 2, 2, 5, 5, 2, 2, 13, 13, 19, 19, 24, 24, 24, 24, 24, 24, 24, 24, 72] 150 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, 42, 43, 44, 45, 46]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456525239 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001456525239 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456525239/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456525239/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456525239 Building ZINC001456731398 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001456731398 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/462 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456731398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731398 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 45, 45, 22, 22, 6, 6, 6, 6, 6, 6, 4, 22, 22, 22, 22, 22, 22, 22, 45, 45, 22, 22, 22, 22] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 463) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/463 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/463' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456731398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731398 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 48, 48, 23, 23, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 48, 48, 23, 23, 23, 23] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 146 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 464) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/464 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/464' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731398.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001456731398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731398 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 45, 45, 22, 22, 6, 6, 6, 6, 6, 6, 4, 22, 22, 22, 22, 22, 22, 22, 45, 45, 22, 22, 22, 22] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 465) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/465 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/465' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731398.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001456731398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731398 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 48, 48, 23, 23, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 48, 48, 23, 23, 23, 23] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 146 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001456731398 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 Building ZINC001456731398 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001456731398 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 462) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456731398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731398 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 45, 45, 22, 22, 6, 6, 6, 6, 6, 6, 4, 22, 22, 22, 22, 22, 22, 22, 45, 45, 22, 22, 22, 22] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 463) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/463: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456731398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731398 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 48, 48, 23, 23, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 48, 48, 23, 23, 23, 23] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 146 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 464) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/464: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731398.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001456731398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731398 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 45, 45, 22, 22, 6, 6, 6, 6, 6, 6, 4, 22, 22, 22, 22, 22, 22, 22, 45, 45, 22, 22, 22, 22] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 465) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731398.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001456731398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731398 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 48, 48, 23, 23, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 48, 48, 23, 23, 23, 23] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 146 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001456731398 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 Building ZINC001456731398 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001456731398 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 462) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456731398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731398 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 45, 45, 22, 22, 6, 6, 6, 6, 6, 6, 4, 22, 22, 22, 22, 22, 22, 22, 45, 45, 22, 22, 22, 22] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 463) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/463: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456731398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731398 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 48, 48, 23, 23, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 48, 48, 23, 23, 23, 23] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 146 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 464) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/464: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731398.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001456731398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731398 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 45, 45, 22, 22, 6, 6, 6, 6, 6, 6, 4, 22, 22, 22, 22, 22, 22, 22, 45, 45, 22, 22, 22, 22] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 465) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731398.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001456731398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731398 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 48, 48, 23, 23, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 48, 48, 23, 23, 23, 23] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 146 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001456731398 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 Building ZINC001456731398 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001456731398 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 462) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456731398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731398 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 45, 45, 22, 22, 6, 6, 6, 6, 6, 6, 4, 22, 22, 22, 22, 22, 22, 22, 45, 45, 22, 22, 22, 22] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 463) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/463: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456731398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731398 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 48, 48, 23, 23, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 48, 48, 23, 23, 23, 23] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 146 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 464) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/464: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731398.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001456731398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731398 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 45, 45, 22, 22, 6, 6, 6, 6, 6, 6, 4, 22, 22, 22, 22, 22, 22, 22, 45, 45, 22, 22, 22, 22] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 465) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731398.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001456731398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731398 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 48, 48, 23, 23, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 48, 48, 23, 23, 23, 23] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 146 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001456731398 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731398 Building ZINC001456731400 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001456731400 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/466 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456731400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731400 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 44, 44, 19, 19, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 44, 44, 19, 19, 19, 19] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 467) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/467 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/467' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456731400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731400 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 42, 42, 20, 20, 6, 6, 6, 6, 6, 6, 4, 20, 20, 20, 20, 20, 20, 20, 42, 42, 20, 20, 20, 20] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 468) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/468 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/468' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731400.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001456731400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731400 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 44, 44, 19, 19, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 44, 44, 19, 19, 19, 19] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 469) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/469 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/469' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731400.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001456731400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731400 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 42, 42, 20, 20, 6, 6, 6, 6, 6, 6, 4, 20, 20, 20, 20, 20, 20, 20, 42, 42, 20, 20, 20, 20] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001456731400 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 Building ZINC001456731400 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001456731400 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 466) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456731400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731400 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 44, 44, 19, 19, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 44, 44, 19, 19, 19, 19] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 467) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/467: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456731400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731400 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 42, 42, 20, 20, 6, 6, 6, 6, 6, 6, 4, 20, 20, 20, 20, 20, 20, 20, 42, 42, 20, 20, 20, 20] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 468) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/468: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731400.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001456731400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731400 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 44, 44, 19, 19, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 44, 44, 19, 19, 19, 19] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 469) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/469: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731400.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001456731400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731400 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 42, 42, 20, 20, 6, 6, 6, 6, 6, 6, 4, 20, 20, 20, 20, 20, 20, 20, 42, 42, 20, 20, 20, 20] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001456731400 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 Building ZINC001456731400 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001456731400 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 466) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456731400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731400 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 44, 44, 19, 19, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 44, 44, 19, 19, 19, 19] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 467) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/467: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456731400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731400 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 42, 42, 20, 20, 6, 6, 6, 6, 6, 6, 4, 20, 20, 20, 20, 20, 20, 20, 42, 42, 20, 20, 20, 20] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 468) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/468: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731400.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001456731400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731400 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 44, 44, 19, 19, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 44, 44, 19, 19, 19, 19] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 469) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/469: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731400.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001456731400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731400 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 42, 42, 20, 20, 6, 6, 6, 6, 6, 6, 4, 20, 20, 20, 20, 20, 20, 20, 42, 42, 20, 20, 20, 20] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001456731400 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 Building ZINC001456731400 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001456731400 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 466) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456731400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731400 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 44, 44, 19, 19, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 44, 44, 19, 19, 19, 19] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 467) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/467: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456731400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731400 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 42, 42, 20, 20, 6, 6, 6, 6, 6, 6, 4, 20, 20, 20, 20, 20, 20, 20, 42, 42, 20, 20, 20, 20] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 468) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/468: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731400.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001456731400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731400 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 44, 44, 19, 19, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 44, 44, 19, 19, 19, 19] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 469) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/469: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1) `ZINC001456731400.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001456731400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001456731400 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCS(=O)(=O)C2(CC(C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 42, 42, 20, 20, 6, 6, 6, 6, 6, 6, 4, 20, 20, 20, 20, 20, 20, 20, 42, 42, 20, 20, 20, 20] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001456731400 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456731400 Building ZINC001456877434 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456877434' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456877434 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456877434 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456877434/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456877434 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/470 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(NC2CCC2)CC1) `ZINC001456877434.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456877434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456877434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001456877434 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(NC2CCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 2, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 12, 13, 13, 13, 5, 5, 2, 2, 2, 2, 7, 7, 2, 5, 5, 5, 5, 5, 12, 13, 13, 13, 13, 13, 13, 13, 5, 5, 5, 5] 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, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456877434 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456877434/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456877434 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 471) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/471 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/471' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(NC2CCC2)CC1) `ZINC001456877434.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456877434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456877434/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001456877434 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(NC2CCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 2, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 9, 13, 13, 13, 4, 4, 2, 2, 2, 2, 7, 7, 2, 4, 4, 4, 4, 4, 9, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4] 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, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 62 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456877434 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001456877434 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456877434/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456877434/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456877434 Building ZINC001456877434 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456877434' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456877434 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456877434 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456877434/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456877434 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 470) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/470: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(NC2CCC2)CC1) `ZINC001456877434.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456877434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456877434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001456877434 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCC(NC2CCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 2, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 12, 13, 13, 13, 5, 5, 2, 2, 2, 2, 7, 7, 2, 5, 5, 5, 5, 5, 12, 13, 13, 13, 13, 13, 13, 13, 5, 5, 5, 5] 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, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456877434 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456877434/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456877434 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 471) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/471: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(NC2CCC2)CC1) `ZINC001456877434.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456877434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456877434/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001456877434 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCC(NC2CCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 2, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 9, 13, 13, 13, 4, 4, 2, 2, 2, 2, 7, 7, 2, 4, 4, 4, 4, 4, 9, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4] 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, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 62 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456877434 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001456877434 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456877434/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456877434/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456877434 Building ZINC001456953360 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953360' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953360 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456953360 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953360/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953360 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/472 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCOC12CCOCC2) `ZINC001456953360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456953360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001456953360 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCOC12CCOCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 6, 6, 6, 2, 1, 1, 1, 1, 3, 3, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 2, 2, 2, 6, 6, 2, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 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, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953360 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953360/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953360 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 473) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/473 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/473' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCOC12CCOCC2) `ZINC001456953360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456953360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001456953360 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCOC12CCOCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 3, 3, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 2, 5, 5, 2, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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, 42, 43, 44, 45]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953360 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001456953360 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953360/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953360/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953360 Building ZINC001456953360 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953360' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953360 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456953360 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953360/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953360 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 472) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/472: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCOC12CCOCC2) `ZINC001456953360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456953360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001456953360 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCOC12CCOCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 6, 6, 6, 2, 1, 1, 1, 1, 3, 3, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 2, 2, 2, 6, 6, 2, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 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, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953360 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953360/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953360 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 473) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/473: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCOC12CCOCC2) `ZINC001456953360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456953360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001456953360 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCOC12CCOCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 3, 3, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 2, 5, 5, 2, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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, 42, 43, 44, 45]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953360 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001456953360 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953360/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953360/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953360 Building ZINC001456953361 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953361' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953361 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456953361 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953361/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953361 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/474 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCOC12CCOCC2) `ZINC001456953361.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456953361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001456953361 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCOC12CCOCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 3, 3, 5, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 2, 5, 5, 2, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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, 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/323031/xbw-8058115.49/working/building/ZINC001456953361 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953361/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953361 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 475) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/475 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/475' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCOC12CCOCC2) `ZINC001456953361.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456953361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953361/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001456953361 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCOC12CCOCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 6, 6, 6, 2, 1, 1, 1, 1, 3, 3, 7, 20, 22, 22, 22, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 6, 6, 2, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 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, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953361 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001456953361 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953361/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953361/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953361 Building ZINC001456953361 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953361' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953361 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456953361 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953361/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953361 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 474) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCOC12CCOCC2) `ZINC001456953361.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456953361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001456953361 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCOC12CCOCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 3, 3, 5, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 2, 5, 5, 2, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 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, 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/323031/xbw-8058115.49/working/building/ZINC001456953361 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953361/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953361 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 475) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCOC12CCOCC2) `ZINC001456953361.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456953361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953361/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001456953361 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCOC12CCOCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 6, 6, 6, 2, 1, 1, 1, 1, 3, 3, 7, 20, 22, 22, 22, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 6, 6, 2, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 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, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953361 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001456953361 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953361/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953361/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001456953361 Building ZINC001457031988 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457031988' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457031988 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457031988 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457031988/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457031988 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/476 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/476' -> `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)N1Cc2nnc(C)n2C[C@@H]1C(=O)N(C)C) `ZINC001457031988.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457031988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457031988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001457031988 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1Cc2nnc(C)n2C[C@@H]1C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14] 20 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 41 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457031988 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457031988/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457031988 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 477) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/477 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/477' -> `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)N1Cc2nnc(C)n2C[C@@H]1C(=O)N(C)C) `ZINC001457031988.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457031988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457031988/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001457031988 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1Cc2nnc(C)n2C[C@@H]1C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18] 23 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 51 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457031988 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001457031988 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457031988/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457031988/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457031988 Building ZINC001457031988 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457031988' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457031988 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457031988 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457031988/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457031988 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 476) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1Cc2nnc(C)n2C[C@@H]1C(=O)N(C)C) `ZINC001457031988.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457031988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457031988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001457031988 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1Cc2nnc(C)n2C[C@@H]1C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14] 20 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 41 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457031988 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457031988/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457031988 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 477) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1Cc2nnc(C)n2C[C@@H]1C(=O)N(C)C) `ZINC001457031988.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457031988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457031988/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001457031988 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1Cc2nnc(C)n2C[C@@H]1C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18] 23 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 51 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457031988 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001457031988 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457031988/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457031988/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457031988 Building ZINC001457032020 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457032020' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457032020 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457032020 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457032020/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457032020 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/478 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/478' -> `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)N1Cc2nnc(C)n2C[C@H]1C(=O)N(C)C) `ZINC001457032020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457032020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457032020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001457032020 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1Cc2nnc(C)n2C[C@H]1C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18] 23 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 51 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457032020 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457032020/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457032020 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 479) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/479 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/479' -> `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)N1Cc2nnc(C)n2C[C@H]1C(=O)N(C)C) `ZINC001457032020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457032020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457032020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001457032020 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1Cc2nnc(C)n2C[C@H]1C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14] 19 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 41 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457032020 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001457032020 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457032020/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457032020/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457032020 Building ZINC001457032020 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457032020' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457032020 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457032020 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457032020/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457032020 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 478) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/478: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1Cc2nnc(C)n2C[C@H]1C(=O)N(C)C) `ZINC001457032020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457032020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457032020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001457032020 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1Cc2nnc(C)n2C[C@H]1C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18] 23 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 51 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457032020 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457032020/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457032020 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 479) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/479: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1Cc2nnc(C)n2C[C@H]1C(=O)N(C)C) `ZINC001457032020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457032020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457032020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001457032020 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1Cc2nnc(C)n2C[C@H]1C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 1, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14] 19 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 41 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457032020 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001457032020 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457032020/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457032020/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457032020 Building ZINC001457178611 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457178611' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457178611 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457178611 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457178611/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457178611 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/480 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCCCCNC(=O)CC1) `ZINC001457178611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457178611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457178611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001457178611 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCCCCNC(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 2, 8, 8, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 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, 42, 43, 44, 45, 46]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457178611 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457178611/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457178611 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 481) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/481 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/481' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCCCCNC(=O)CC1) `ZINC001457178611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457178611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457178611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001457178611 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCCCCNC(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 8, 4, 1, 1, 1, 1, 8, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 8, 8, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 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, 42, 43, 44, 45, 46]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457178611 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001457178611 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457178611/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457178611/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457178611 Building ZINC001457178611 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457178611' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457178611 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457178611 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457178611/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457178611 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 480) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCCCCNC(=O)CC1) `ZINC001457178611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457178611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457178611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001457178611 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCCCCNC(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 1, 8, 10, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 2, 8, 8, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 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, 42, 43, 44, 45, 46]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457178611 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457178611/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457178611 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 481) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCCCCNC(=O)CC1) `ZINC001457178611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457178611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457178611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001457178611 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCCCCNC(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 6, 6, 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, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 8, 4, 1, 1, 1, 1, 8, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 4, 4, 4, 8, 8, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 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, 42, 43, 44, 45, 46]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457178611 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001457178611 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457178611/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457178611/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001457178611 Building ZINC001461160067 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160067' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160067 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461160067 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160067/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160067 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/482 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@]2(CCS(=O)(=O)C2)C1) `ZINC001461160067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461160067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001461160067 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@]2(CCS(=O)(=O)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', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 9, 13, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4, 4, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 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]) total number of confs: 59 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160067 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160067/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160067 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 483) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/483 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/483' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCO[C@@]2(CCS(=O)(=O)C2)C1) `ZINC001461160067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461160067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001461160067 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCO[C@@]2(CCS(=O)(=O)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', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 10, 14, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 4, 4, 4, 4, 4, 4, 4, 4, 4, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37] 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]) total number of confs: 64 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160067 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001461160067 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160067/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160067/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160067 Building ZINC001461160067 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160067' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160067 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461160067 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160067/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160067 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 482) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/482: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@]2(CCS(=O)(=O)C2)C1) `ZINC001461160067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461160067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001461160067 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@]2(CCS(=O)(=O)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', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 9, 13, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4, 4, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 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]) total number of confs: 59 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160067 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160067/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160067 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 483) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/483: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCO[C@@]2(CCS(=O)(=O)C2)C1) `ZINC001461160067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461160067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001461160067 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCO[C@@]2(CCS(=O)(=O)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', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 10, 14, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 4, 4, 4, 4, 4, 4, 4, 4, 4, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37] 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]) total number of confs: 64 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160067 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001461160067 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160067/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160067/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160067 Building ZINC001461160068 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160068' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461160068 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160068/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/484 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCO[C@]2(CCS(=O)(=O)C2)C1) `ZINC001461160068.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461160068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001461160068 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCO[C@]2(CCS(=O)(=O)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', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 9, 17, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 62 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160068/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 485) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/485 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/485' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCO[C@]2(CCS(=O)(=O)C2)C1) `ZINC001461160068.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461160068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001461160068 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCO[C@]2(CCS(=O)(=O)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', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 9, 18, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 4, 4, 4, 4, 4, 4, 4, 4, 4, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37] 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]) total number of confs: 61 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001461160068 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160068/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160068/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160068 Building ZINC001461160068 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160068' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461160068 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160068/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 484) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCO[C@]2(CCS(=O)(=O)C2)C1) `ZINC001461160068.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461160068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001461160068 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCO[C@]2(CCS(=O)(=O)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', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 9, 17, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 62 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160068/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 485) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCO[C@]2(CCS(=O)(=O)C2)C1) `ZINC001461160068.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461160068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001461160068 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCO[C@]2(CCS(=O)(=O)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', 'O.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 9, 18, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 4, 4, 4, 4, 4, 4, 4, 4, 4, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37] 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]) total number of confs: 61 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001461160068 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160068/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160068/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001461160068 Building ZINC001462317219 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001462317219' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001462317219 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462317219 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001462317219/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001462317219 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/486 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCS(=O)(=O)CC1) `ZINC001462317219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462317219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001462317219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001462317219 none NC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 14, 11, 11, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 25, 11, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 25, 25, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001462317219 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001462317219/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001462317219 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 487) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/487 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/487' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCS(=O)(=O)CC1) `ZINC001462317219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462317219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001462317219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001462317219 none NC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 14, 11, 11, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 20, 24, 11, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 24, 24, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001462317219 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001462317219 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001462317219/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001462317219/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001462317219 Building ZINC001462317219 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001462317219' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001462317219 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462317219 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001462317219/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001462317219 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 486) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/486: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCS(=O)(=O)CC1) `ZINC001462317219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462317219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001462317219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001462317219 none NC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 14, 11, 11, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 25, 11, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 25, 25, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001462317219 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001462317219/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001462317219 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 487) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/487: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCS(=O)(=O)CC1) `ZINC001462317219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462317219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001462317219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001462317219 none NC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 14, 11, 11, 5, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 20, 24, 11, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 24, 24, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001462317219 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001462317219 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001462317219/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001462317219/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001462317219 Building ZINC001464477995 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001464477995' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001464477995 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464477995 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001464477995/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001464477995 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/488 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1cn2ccsc2n1) `ZINC001464477995.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464477995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001464477995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001464477995 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1cn2ccsc2n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 1, 14, 1, 8, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 3, 1, 1, 1, 1, 3, 3, 3, 14, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 6, 6, 3, 3, 14, 14, 19, 19, 19] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001464477995 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001464477995/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001464477995 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 489) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/489 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/489' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1cn2ccsc2n1) `ZINC001464477995.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464477995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001464477995/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001464477995 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1cn2ccsc2n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 1, 14, 1, 8, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 3, 1, 1, 1, 1, 3, 3, 3, 14, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 6, 6, 3, 3, 14, 14, 19, 19, 19] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001464477995 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001464477995 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001464477995/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001464477995/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001464477995 Building ZINC001464477995 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001464477995' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001464477995 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464477995 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001464477995/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001464477995 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 488) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/488: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1cn2ccsc2n1) `ZINC001464477995.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464477995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001464477995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001464477995 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1cn2ccsc2n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 1, 14, 1, 8, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 3, 1, 1, 1, 1, 3, 3, 3, 14, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 6, 6, 3, 3, 14, 14, 19, 19, 19] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001464477995 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001464477995/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001464477995 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 489) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/489: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1cn2ccsc2n1) `ZINC001464477995.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464477995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001464477995/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001464477995 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1cn2ccsc2n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 1, 14, 1, 8, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 3, 1, 1, 1, 1, 3, 3, 3, 14, 19, 19, 19, 19, 19, 19, 19, 3, 3, 3, 3, 6, 6, 3, 3, 14, 14, 19, 19, 19] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001464477995 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001464477995 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001464477995/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001464477995/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001464477995 Building ZINC001466082929 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082929' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082929 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466082929 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082929/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082929 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/490 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@H](CN(C)C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001466082929.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466082929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001466082929 none CC(=O)N1CC[C@H](CN(C)C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 16, 15, 15, 15, 11, 15, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 6, 6, 6, 2, 2, 2, 15, 16, 16, 16, 15, 15, 15, 15, 9, 9, 3, 3, 3, 2, 6, 6, 2, 2, 2, 2, 15, 15] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082929 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082929/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082929 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 491) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/491 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/491' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@H](CN(C)C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001466082929.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466082929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001466082929 none CC(=O)N1CC[C@H](CN(C)C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 15, 14, 14, 14, 11, 14, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 14, 15, 15, 15, 14, 14, 14, 14, 7, 7, 3, 3, 3, 2, 5, 5, 2, 2, 2, 2, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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/323031/xbw-8058115.49/working/building/ZINC001466082929 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001466082929 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082929/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082929/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082929 Building ZINC001466082929 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082929' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082929 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466082929 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082929/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082929 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 490) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/490: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@H](CN(C)C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001466082929.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466082929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001466082929 none CC(=O)N1CC[C@H](CN(C)C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 16, 15, 15, 15, 11, 15, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 6, 6, 6, 2, 2, 2, 15, 16, 16, 16, 15, 15, 15, 15, 9, 9, 3, 3, 3, 2, 6, 6, 2, 2, 2, 2, 15, 15] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082929 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082929/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082929 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 491) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/491: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@H](CN(C)C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001466082929.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466082929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001466082929 none CC(=O)N1CC[C@H](CN(C)C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 15, 14, 14, 14, 11, 14, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 14, 15, 15, 15, 14, 14, 14, 14, 7, 7, 3, 3, 3, 2, 5, 5, 2, 2, 2, 2, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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/323031/xbw-8058115.49/working/building/ZINC001466082929 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001466082929 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082929/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082929/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082929 Building ZINC001466082930 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082930' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082930 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466082930 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082930/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082930 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/492 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@@H](CN(C)C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001466082930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466082930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001466082930 none CC(=O)N1CC[C@@H](CN(C)C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 16, 17, 16, 16, 16, 12, 16, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 16, 17, 17, 17, 16, 16, 16, 16, 9, 9, 4, 4, 4, 1, 4, 4, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [43, 38, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 45, 46]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082930 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082930/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082930 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 493) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/493 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/493' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@@H](CN(C)C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001466082930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466082930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001466082930 none CC(=O)N1CC[C@@H](CN(C)C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 16, 15, 15, 15, 11, 15, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 15, 16, 16, 16, 15, 15, 15, 15, 9, 9, 3, 3, 3, 2, 5, 5, 2, 2, 2, 2, 15, 15] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082930 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001466082930 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082930/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082930/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082930 Building ZINC001466082930 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082930' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082930 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466082930 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082930/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082930 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 492) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/492: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@@H](CN(C)C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001466082930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466082930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001466082930 none CC(=O)N1CC[C@@H](CN(C)C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 16, 17, 16, 16, 16, 12, 16, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 16, 17, 17, 17, 16, 16, 16, 16, 9, 9, 4, 4, 4, 1, 4, 4, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [43, 38, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 45, 46]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082930 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082930/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082930 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 493) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/493: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@@H](CN(C)C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001466082930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466082930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001466082930 none CC(=O)N1CC[C@@H](CN(C)C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 16, 15, 15, 15, 11, 15, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 15, 16, 16, 16, 15, 15, 15, 15, 9, 9, 3, 3, 3, 2, 5, 5, 2, 2, 2, 2, 15, 15] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082930 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001466082930 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082930/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082930/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466082930 Building ZINC001466117171 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466117171' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466117171 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466117171 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466117171/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466117171 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/494 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC(=O)c1cccs1) `ZINC001466117171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466117171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466117171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001466117171 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC(=O)c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations 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, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 14, 29, 29, 34, 34, 34, 34, 1, 1, 1, 1, 3, 3, 1, 2, 14, 14, 34, 34, 34] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 23, 24, 25, 26, 29] set([32, 33, 34, 35, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 30, 31]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466117171 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466117171/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466117171 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 495) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/495 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/495' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC(=O)c1cccs1) `ZINC001466117171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466117171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466117171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001466117171 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC(=O)c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations 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, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 14, 28, 28, 33, 33, 33, 33, 1, 1, 1, 1, 3, 3, 1, 2, 14, 14, 33, 33, 33] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 23, 24, 25, 26, 29] set([32, 33, 34, 35, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 30, 31]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466117171 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001466117171 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466117171/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466117171/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466117171 Building ZINC001466117171 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466117171' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466117171 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466117171 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466117171/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466117171 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 494) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/494: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC(=O)c1cccs1) `ZINC001466117171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466117171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466117171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001466117171 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCC(=O)c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations 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, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 14, 29, 29, 34, 34, 34, 34, 1, 1, 1, 1, 3, 3, 1, 2, 14, 14, 34, 34, 34] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 23, 24, 25, 26, 29] set([32, 33, 34, 35, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 30, 31]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466117171 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466117171/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466117171 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 495) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/495: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC(=O)c1cccs1) `ZINC001466117171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466117171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466117171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001466117171 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCC(=O)c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations 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, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 14, 28, 28, 33, 33, 33, 33, 1, 1, 1, 1, 3, 3, 1, 2, 14, 14, 33, 33, 33] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 23, 24, 25, 26, 29] set([32, 33, 34, 35, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 30, 31]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466117171 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001466117171 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466117171/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466117171/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466117171 Building ZINC001466855955 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855955' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855955 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466855955 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855955/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855955 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/496 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@]1=O) `ZINC001466855955.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466855955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001466855955 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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] 0 hydrogens 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, 10, 1, 11, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 8, 8, 2, 2, 2, 2, 13, 13, 13, 13] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855955 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855955/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855955 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 497) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/497 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/497' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@]1=O) `ZINC001466855955.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466855955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855955/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001466855955 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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] 0 hydrogens 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, 11, 1, 12, 1, 1, 1, 3, 3, 3, 10, 10, 10, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 10, 10, 3, 3, 3, 3, 13, 13, 13, 13] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855955 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001466855955 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855955/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855955/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855955 Building ZINC001466855955 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855955' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855955 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466855955 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855955/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855955 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 496) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/496: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@]1=O) `ZINC001466855955.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466855955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001466855955 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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] 0 hydrogens 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, 10, 1, 11, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 8, 8, 2, 2, 2, 2, 13, 13, 13, 13] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855955 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855955/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855955 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 497) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/497: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@]1=O) `ZINC001466855955.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466855955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855955/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001466855955 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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] 0 hydrogens 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, 11, 1, 12, 1, 1, 1, 3, 3, 3, 10, 10, 10, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 10, 10, 3, 3, 3, 3, 13, 13, 13, 13] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855955 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001466855955 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855955/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855955/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855955 Building ZINC001466855956 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855956' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855956 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466855956 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855956/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855956 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/498 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@]1=O) `ZINC001466855956.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466855956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001466855956 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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] 0 hydrogens 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, 10, 1, 9, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 8, 8, 2, 2, 2, 2, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855956 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855956/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855956 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 499) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/499 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/499' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@]1=O) `ZINC001466855956.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466855956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855956/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001466855956 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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] 0 hydrogens 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, 6, 2, 6, 1, 1, 1, 3, 3, 3, 11, 11, 11, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 11, 11, 3, 3, 3, 3, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 60 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855956 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001466855956 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855956/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855956/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855956 Building ZINC001466855956 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855956' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855956 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466855956 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855956/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855956 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 498) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/498: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@]1=O) `ZINC001466855956.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466855956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001466855956 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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] 0 hydrogens 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, 10, 1, 9, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 8, 8, 2, 2, 2, 2, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855956 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855956/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855956 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 499) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/499: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@]1=O) `ZINC001466855956.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466855956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855956/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001466855956 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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] 0 hydrogens 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, 6, 2, 6, 1, 1, 1, 3, 3, 3, 11, 11, 11, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 11, 11, 3, 3, 3, 3, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 60 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855956 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001466855956 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855956/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855956/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855956 Building ZINC001466855957 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855957' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855957 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466855957 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855957/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855957 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/500 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@@]1=O) `ZINC001466855957.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466855957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001466855957 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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] 0 hydrogens 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, 8, 1, 10, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 8, 8, 2, 2, 2, 2, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855957 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855957/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855957 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 501) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/501 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/501' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@@]1=O) `ZINC001466855957.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466855957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855957/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001466855957 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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] 0 hydrogens 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, 10, 1, 11, 1, 1, 1, 3, 3, 3, 9, 9, 9, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 9, 9, 3, 3, 3, 3, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855957 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001466855957 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855957/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855957/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855957 Building ZINC001466855957 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855957' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855957 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466855957 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855957/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855957 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 500) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/500: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@@]1=O) `ZINC001466855957.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466855957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001466855957 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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] 0 hydrogens 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, 8, 1, 10, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 8, 8, 2, 2, 2, 2, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855957 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855957/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855957 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 501) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/501: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@@]1=O) `ZINC001466855957.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466855957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855957/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001466855957 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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] 0 hydrogens 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, 10, 1, 11, 1, 1, 1, 3, 3, 3, 9, 9, 9, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 9, 9, 3, 3, 3, 3, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855957 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001466855957 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855957/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855957/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855957 Building ZINC001466855958 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855958' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855958 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466855958 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855958/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855958 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/502 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@@]1=O) `ZINC001466855958.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466855958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001466855958 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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] 0 hydrogens 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, 11, 1, 13, 1, 1, 1, 3, 3, 3, 10, 10, 10, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 10, 10, 3, 3, 3, 3, 13, 13, 13, 13] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855958 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855958/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855958 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 503) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/503 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/503' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@@]1=O) `ZINC001466855958.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466855958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001466855958 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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] 0 hydrogens 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, 10, 1, 11, 1, 1, 1, 3, 3, 3, 11, 11, 11, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 3, 11, 11, 3, 3, 3, 3, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855958 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001466855958 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855958/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855958/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855958 Building ZINC001466855958 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855958' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855958 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466855958 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855958/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855958 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 502) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/502: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@@]1=O) `ZINC001466855958.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466855958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001466855958 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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] 0 hydrogens 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, 11, 1, 13, 1, 1, 1, 3, 3, 3, 10, 10, 10, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 10, 10, 3, 3, 3, 3, 13, 13, 13, 13] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855958 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855958/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855958 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 503) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/503: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@@]1=O) `ZINC001466855958.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466855958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001466855958 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)CC[S@@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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] 0 hydrogens 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, 10, 1, 11, 1, 1, 1, 3, 3, 3, 11, 11, 11, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 3, 11, 11, 3, 3, 3, 3, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855958 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001466855958 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855958/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855958/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466855958 Building ZINC001466884440 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884440' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884440 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466884440 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884440/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884440 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/504 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1c2nncn2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001466884440.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466884440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001466884440 none C[C@@H]1c2nncn2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 1, 7, 1, 1, 1, 7, 7, 7, 23, 23, 23, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 7, 23, 23, 7, 7, 7, 7] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 92 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884440 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884440/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884440 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 505) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/505 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/505' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1c2nncn2CCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001466884440.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466884440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884440/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001466884440 none C[C@@H]1c2nncn2CCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 1, 7, 1, 1, 1, 7, 7, 7, 24, 24, 24, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 7, 24, 24, 7, 7, 7, 7] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 95 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884440 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001466884440 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884440/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884440/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884440 Building ZINC001466884440 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884440' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884440 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466884440 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884440/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884440 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 504) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/504: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1c2nncn2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001466884440.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466884440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001466884440 none C[C@@H]1c2nncn2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 1, 7, 1, 1, 1, 7, 7, 7, 23, 23, 23, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 7, 23, 23, 7, 7, 7, 7] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 92 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884440 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884440/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884440 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 505) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/505: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1c2nncn2CCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001466884440.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466884440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884440/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001466884440 none C[C@@H]1c2nncn2CCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 1, 7, 1, 1, 1, 7, 7, 7, 24, 24, 24, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 7, 24, 24, 7, 7, 7, 7] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 95 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884440 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001466884440 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884440/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884440/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884440 Building ZINC001466884441 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884441' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884441 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466884441 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884441/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884441 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/506 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1c2nncn2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001466884441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466884441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001466884441 none C[C@H]1c2nncn2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 1, 7, 1, 1, 1, 6, 6, 6, 21, 21, 21, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 6, 21, 21, 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]) total number of confs: 88 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884441 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884441/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884441 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 507) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/507 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/507' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1c2nncn2CCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001466884441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466884441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001466884441 none C[C@H]1c2nncn2CCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 1, 7, 1, 1, 1, 7, 7, 7, 26, 26, 26, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 7, 26, 26, 7, 7, 7, 7] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 104 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884441 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001466884441 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884441/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884441/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884441 Building ZINC001466884441 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884441' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884441 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466884441 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884441/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884441 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 506) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/506: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1c2nncn2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001466884441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466884441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001466884441 none C[C@H]1c2nncn2CCN1C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 1, 7, 1, 1, 1, 6, 6, 6, 21, 21, 21, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 6, 21, 21, 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]) total number of confs: 88 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884441 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884441/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884441 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 507) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/507: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1c2nncn2CCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001466884441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466884441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001466884441 none C[C@H]1c2nncn2CCN1C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 1, 7, 1, 1, 1, 7, 7, 7, 26, 26, 26, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 7, 26, 26, 7, 7, 7, 7] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 104 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884441 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001466884441 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884441/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884441/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001466884441 Building ZINC001467853266 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001467853266' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001467853266 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467853266 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001467853266/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001467853266 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/508 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)CCOCCNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001467853266.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467853266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001467853266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001467853266 none NS(=O)(=O)CCOCCNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 27, 36, 36, 27, 20, 15, 10, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 36, 36, 27, 27, 27, 27, 15, 15, 10, 10, 5, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 159 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001467853266 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001467853266/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001467853266 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 509) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/509 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/509' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)CCOCCNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001467853266.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467853266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001467853266/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001467853266 none NS(=O)(=O)CCOCCNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 27, 36, 36, 27, 20, 15, 10, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 36, 36, 27, 27, 27, 27, 15, 15, 10, 10, 5, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 159 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001467853266 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001467853266 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001467853266/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001467853266/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001467853266 Building ZINC001467853266 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001467853266' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001467853266 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467853266 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001467853266/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001467853266 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 508) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/508: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)CCOCCNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001467853266.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467853266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001467853266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001467853266 none NS(=O)(=O)CCOCCNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 27, 36, 36, 27, 20, 15, 10, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 36, 36, 27, 27, 27, 27, 15, 15, 10, 10, 5, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 159 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001467853266 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001467853266/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001467853266 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 509) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)CCOCCNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001467853266.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467853266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001467853266/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001467853266 none NS(=O)(=O)CCOCCNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 27, 36, 36, 27, 20, 15, 10, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 36, 36, 27, 27, 27, 27, 15, 15, 10, 10, 5, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 159 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001467853266 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001467853266 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001467853266/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001467853266/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001467853266 Building ZINC001468626878 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468626878' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468626878 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468626878 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468626878/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468626878 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/510 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1nccc(C(F)F)n1) `ZINC001468626878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468626878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468626878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001468626878 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1nccc(C(F)F)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 5, 15, 15, 8, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 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: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 7, 30, 30, 7, 30, 30, 35, 35, 30, 1, 1, 1, 1, 3, 3, 1, 2, 7, 7, 30, 8, 35] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 25, 26, 27, 28, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 32, 33, 34, 35, 36, 37]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468626878 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468626878/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468626878 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 511) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/511 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/511' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1nccc(C(F)F)n1) `ZINC001468626878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468626878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468626878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001468626878 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1nccc(C(F)F)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 5, 15, 15, 8, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 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: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 7, 30, 30, 10, 30, 30, 35, 35, 30, 1, 1, 1, 1, 3, 3, 1, 2, 7, 7, 30, 30, 35] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 25, 26, 27, 28, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 32, 33, 34, 35, 36, 37]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468626878 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001468626878 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468626878/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468626878/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468626878 Building ZINC001468626878 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468626878' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468626878 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468626878 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468626878/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468626878 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 510) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/510: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1nccc(C(F)F)n1) `ZINC001468626878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468626878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468626878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001468626878 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NCc1nccc(C(F)F)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 5, 15, 15, 8, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 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: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 7, 30, 30, 7, 30, 30, 35, 35, 30, 1, 1, 1, 1, 3, 3, 1, 2, 7, 7, 30, 8, 35] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 25, 26, 27, 28, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 32, 33, 34, 35, 36, 37]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468626878 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468626878/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468626878 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 511) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/511: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1nccc(C(F)F)n1) `ZINC001468626878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468626878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468626878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001468626878 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NCc1nccc(C(F)F)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 5, 15, 15, 8, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 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: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 7, 30, 30, 10, 30, 30, 35, 35, 30, 1, 1, 1, 1, 3, 3, 1, 2, 7, 7, 30, 30, 35] 50 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 25, 26, 27, 28, 31] set([5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 32, 33, 34, 35, 36, 37]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468626878 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001468626878 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468626878/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468626878/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468626878 Building ZINC001468771282 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001468771282 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/512 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1) `ZINC001468771282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468771282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771282 none CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 10, 1, 10, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 4, 4, 11, 11, 11, 11, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 4, 13, 13, 4, 4, 4, 4, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 69 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 513) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/513 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/513' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1) `ZINC001468771282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468771282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771282 none CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 10, 1, 10, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 4, 4, 11, 11, 11, 11, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 4, 13, 13, 4, 4, 4, 4, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 69 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 514) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/514 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/514' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1) `ZINC001468771282.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001468771282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771282 none CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 1, 11, 1, 1, 1, 3, 3, 3, 12, 12, 12, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 12, 12, 3, 3, 3, 3, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 63 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 515) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/515 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/515' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1) `ZINC001468771282.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001468771282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771282 none CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 1, 11, 1, 1, 1, 3, 3, 3, 12, 12, 12, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 12, 12, 3, 3, 3, 3, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 63 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001468771282 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 Building ZINC001468771282 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001468771282 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 512) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/512: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1) `ZINC001468771282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468771282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771282 none CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 10, 1, 10, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 4, 4, 11, 11, 11, 11, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 4, 13, 13, 4, 4, 4, 4, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 69 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 513) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/513: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1) `ZINC001468771282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468771282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771282 none CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 10, 1, 10, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 4, 4, 11, 11, 11, 11, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 4, 13, 13, 4, 4, 4, 4, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 69 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 514) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/514: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1) `ZINC001468771282.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001468771282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771282 none CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 1, 11, 1, 1, 1, 3, 3, 3, 12, 12, 12, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 12, 12, 3, 3, 3, 3, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 63 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 515) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/515: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1) `ZINC001468771282.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001468771282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771282 none CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 1, 11, 1, 1, 1, 3, 3, 3, 12, 12, 12, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 12, 12, 3, 3, 3, 3, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 63 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001468771282 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 Building ZINC001468771282 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001468771282 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 512) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/512: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1) `ZINC001468771282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468771282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771282 none CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 10, 1, 10, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 4, 4, 11, 11, 11, 11, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 4, 13, 13, 4, 4, 4, 4, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 69 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 513) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/513: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1) `ZINC001468771282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468771282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771282 none CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 10, 1, 10, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 4, 4, 11, 11, 11, 11, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 4, 13, 13, 4, 4, 4, 4, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 69 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 514) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/514: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1) `ZINC001468771282.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001468771282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771282 none CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 1, 11, 1, 1, 1, 3, 3, 3, 12, 12, 12, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 12, 12, 3, 3, 3, 3, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 63 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 515) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/515: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1) `ZINC001468771282.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001468771282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771282 none CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 1, 11, 1, 1, 1, 3, 3, 3, 12, 12, 12, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 12, 12, 3, 3, 3, 3, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 63 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001468771282 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 Building ZINC001468771282 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001468771282 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 512) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/512: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1) `ZINC001468771282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468771282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771282 none CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 10, 1, 10, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 4, 4, 11, 11, 11, 11, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 4, 13, 13, 4, 4, 4, 4, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 69 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 513) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/513: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1) `ZINC001468771282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468771282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771282 none CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 10, 1, 10, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 4, 4, 11, 11, 11, 11, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 4, 13, 13, 4, 4, 4, 4, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 69 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 514) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/514: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1) `ZINC001468771282.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001468771282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771282 none CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 1, 11, 1, 1, 1, 3, 3, 3, 12, 12, 12, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 12, 12, 3, 3, 3, 3, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 63 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 515) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/515: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1) `ZINC001468771282.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001468771282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771282 none CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 1, 11, 1, 1, 1, 3, 3, 3, 12, 12, 12, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 12, 12, 3, 3, 3, 3, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 63 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001468771282 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771282 Building ZINC001468771284 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001468771284 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/516 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1) `ZINC001468771284.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468771284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771284 none CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 10, 1, 9, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 4, 4, 11, 11, 11, 11, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 4, 13, 13, 4, 4, 4, 4, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 517) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/517 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/517' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1) `ZINC001468771284.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468771284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771284 none CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 10, 1, 9, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 4, 4, 11, 11, 11, 11, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 4, 13, 13, 4, 4, 4, 4, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 518) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/518 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/518' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1) `ZINC001468771284.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001468771284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771284 none CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 12, 12, 12, 12, 12, 9, 1, 10, 1, 1, 1, 4, 4, 4, 14, 14, 14, 4, 4, 4, 12, 12, 12, 12, 13, 13, 13, 13, 13, 12, 12, 12, 12, 12, 12, 4, 14, 14, 4, 4, 4, 4, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 77 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 519) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/519 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/519' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1) `ZINC001468771284.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001468771284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771284 none CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 12, 12, 12, 12, 12, 9, 1, 10, 1, 1, 1, 4, 4, 4, 14, 14, 14, 4, 4, 4, 12, 12, 12, 12, 13, 13, 13, 13, 13, 12, 12, 12, 12, 12, 12, 4, 14, 14, 4, 4, 4, 4, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 77 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001468771284 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 Building ZINC001468771284 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001468771284 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 516) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/516: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1) `ZINC001468771284.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468771284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771284 none CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 10, 1, 9, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 4, 4, 11, 11, 11, 11, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 4, 13, 13, 4, 4, 4, 4, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 517) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/517: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1) `ZINC001468771284.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468771284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771284 none CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 10, 1, 9, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 4, 4, 11, 11, 11, 11, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 4, 13, 13, 4, 4, 4, 4, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 518) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/518: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1) `ZINC001468771284.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001468771284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771284 none CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 12, 12, 12, 12, 12, 9, 1, 10, 1, 1, 1, 4, 4, 4, 14, 14, 14, 4, 4, 4, 12, 12, 12, 12, 13, 13, 13, 13, 13, 12, 12, 12, 12, 12, 12, 4, 14, 14, 4, 4, 4, 4, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 77 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 519) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/519: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1) `ZINC001468771284.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001468771284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771284 none CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 12, 12, 12, 12, 12, 9, 1, 10, 1, 1, 1, 4, 4, 4, 14, 14, 14, 4, 4, 4, 12, 12, 12, 12, 13, 13, 13, 13, 13, 12, 12, 12, 12, 12, 12, 4, 14, 14, 4, 4, 4, 4, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 77 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001468771284 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 Building ZINC001468771284 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001468771284 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 516) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/516: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1) `ZINC001468771284.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468771284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771284 none CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 10, 1, 9, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 4, 4, 11, 11, 11, 11, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 4, 13, 13, 4, 4, 4, 4, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 517) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/517: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1) `ZINC001468771284.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468771284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771284 none CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 10, 1, 9, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 4, 4, 11, 11, 11, 11, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 4, 13, 13, 4, 4, 4, 4, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 518) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/518: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1) `ZINC001468771284.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001468771284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771284 none CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 12, 12, 12, 12, 12, 9, 1, 10, 1, 1, 1, 4, 4, 4, 14, 14, 14, 4, 4, 4, 12, 12, 12, 12, 13, 13, 13, 13, 13, 12, 12, 12, 12, 12, 12, 4, 14, 14, 4, 4, 4, 4, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 77 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 519) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/519: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1) `ZINC001468771284.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001468771284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771284 none CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 12, 12, 12, 12, 12, 9, 1, 10, 1, 1, 1, 4, 4, 4, 14, 14, 14, 4, 4, 4, 12, 12, 12, 12, 13, 13, 13, 13, 13, 12, 12, 12, 12, 12, 12, 4, 14, 14, 4, 4, 4, 4, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 77 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001468771284 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 Building ZINC001468771284 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001468771284 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 516) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/516: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1) `ZINC001468771284.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468771284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771284 none CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 10, 1, 9, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 4, 4, 11, 11, 11, 11, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 4, 13, 13, 4, 4, 4, 4, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 517) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/517: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1) `ZINC001468771284.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468771284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771284 none CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 10, 1, 9, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 4, 4, 11, 11, 11, 11, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 4, 13, 13, 4, 4, 4, 4, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 518) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/518: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1) `ZINC001468771284.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001468771284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771284 none CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 12, 12, 12, 12, 12, 9, 1, 10, 1, 1, 1, 4, 4, 4, 14, 14, 14, 4, 4, 4, 12, 12, 12, 12, 13, 13, 13, 13, 13, 12, 12, 12, 12, 12, 12, 4, 14, 14, 4, 4, 4, 4, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 77 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 519) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/519: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1) `ZINC001468771284.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001468771284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001468771284 none CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 12, 12, 12, 12, 12, 9, 1, 10, 1, 1, 1, 4, 4, 4, 14, 14, 14, 4, 4, 4, 12, 12, 12, 12, 13, 13, 13, 13, 13, 12, 12, 12, 12, 12, 12, 4, 14, 14, 4, 4, 4, 4, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 77 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001468771284 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468771284 Building ZINC001468893102 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468893102' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468893102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468893102 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468893102/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468893102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/520 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)NC(C)C)CC1) `ZINC001468893102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468893102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468893102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001468893102 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)NC(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 8, 15, 15, 15, 15, 28, 28, 28, 38, 38, 38, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 38, 38, 38, 38, 38, 38, 38, 38, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468893102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468893102/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468893102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 521) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/521 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/521' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)NC(C)C)CC1) `ZINC001468893102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468893102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468893102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001468893102 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)NC(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 8, 15, 15, 15, 15, 25, 25, 25, 34, 34, 34, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 34, 34, 34, 34, 34, 34, 34, 34, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468893102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001468893102 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468893102/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468893102/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468893102 Building ZINC001468893102 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468893102' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468893102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468893102 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468893102/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468893102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 520) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/520: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)NC(C)C)CC1) `ZINC001468893102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468893102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468893102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001468893102 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)NC(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 8, 15, 15, 15, 15, 28, 28, 28, 38, 38, 38, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 38, 38, 38, 38, 38, 38, 38, 38, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468893102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468893102/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468893102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 521) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/521: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)NC(C)C)CC1) `ZINC001468893102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468893102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468893102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001468893102 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(S(=O)(=O)NC(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 8, 15, 15, 15, 15, 25, 25, 25, 34, 34, 34, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 34, 34, 34, 34, 34, 34, 34, 34, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468893102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001468893102 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468893102/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468893102/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001468893102 Building ZINC001469551700 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551700' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551700 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469551700 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551700/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551700 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/522 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H]1C(F)(F)F) `ZINC001469551700.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469551700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001469551700 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need 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, 24, 24, 24, 6, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 24, 24, 6, 8, 8, 8, 8] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551700 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551700/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551700 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 523) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/523 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/523' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H]1C(F)(F)F) `ZINC001469551700.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469551700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551700/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001469551700 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need 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, 20, 20, 20, 6, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 6, 6, 20, 20, 6, 9, 9, 9, 9] 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]) total number of confs: 80 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551700 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001469551700 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551700/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551700/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551700 Building ZINC001469551700 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551700' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551700 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469551700 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551700/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551700 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 522) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/522: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H]1C(F)(F)F) `ZINC001469551700.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469551700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001469551700 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need 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, 24, 24, 24, 6, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 24, 24, 6, 8, 8, 8, 8] 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551700 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551700/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551700 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 523) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/523: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H]1C(F)(F)F) `ZINC001469551700.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469551700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551700/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001469551700 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need 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, 20, 20, 20, 6, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 6, 6, 20, 20, 6, 9, 9, 9, 9] 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]) total number of confs: 80 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551700 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001469551700 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551700/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551700/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551700 Building ZINC001469551701 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551701' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551701 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469551701 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551701/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551701 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/524 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H]1C(F)(F)F) `ZINC001469551701.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469551701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001469551701 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need 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, 21, 21, 21, 6, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6, 21, 21, 6, 10, 10, 10, 10] 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]) total number of confs: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551701 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551701/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551701 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 525) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/525 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/525' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H]1C(F)(F)F) `ZINC001469551701.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469551701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551701/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001469551701 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need 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, 21, 21, 21, 6, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 21, 21, 6, 8, 8, 8, 8] 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551701 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001469551701 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551701/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551701/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551701 Building ZINC001469551701 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551701' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551701 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469551701 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551701/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551701 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 524) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/524: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H]1C(F)(F)F) `ZINC001469551701.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469551701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001469551701 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need 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, 21, 21, 21, 6, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6, 21, 21, 6, 10, 10, 10, 10] 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]) total number of confs: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551701 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551701/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551701 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 525) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/525: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H]1C(F)(F)F) `ZINC001469551701.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469551701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551701/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001469551701 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 15, 15, 15, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need 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, 21, 21, 21, 6, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 21, 21, 6, 8, 8, 8, 8] 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551701 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001469551701 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551701/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551701/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001469551701 Building ZINC001471012358 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012358' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012358 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471012358 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012358/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012358 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/526 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](C(F)F)CC1) `ZINC001471012358.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471012358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471012358 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](C(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 15, 15, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 7, 9, 14, 14, 14, 14, 14, 14, 19, 19, 14, 14, 2, 2, 2, 2, 8, 8, 2, 14, 14, 14, 14, 19, 14, 14, 14, 14] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012358 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012358/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012358 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 527) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/527 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/527' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](C(F)F)CC1) `ZINC001471012358.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471012358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471012358 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](C(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 15, 15, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 6, 9, 12, 12, 12, 12, 12, 12, 18, 18, 12, 12, 2, 2, 2, 2, 8, 8, 2, 12, 12, 12, 12, 18, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012358 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471012358 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012358/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012358/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012358 Building ZINC001471012358 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012358' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012358 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471012358 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012358/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012358 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 526) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/526: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](C(F)F)CC1) `ZINC001471012358.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471012358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471012358 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](C(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 15, 15, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 7, 9, 14, 14, 14, 14, 14, 14, 19, 19, 14, 14, 2, 2, 2, 2, 8, 8, 2, 14, 14, 14, 14, 19, 14, 14, 14, 14] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012358 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012358/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012358 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 527) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/527: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](C(F)F)CC1) `ZINC001471012358.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471012358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471012358 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](C(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 15, 15, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 6, 9, 12, 12, 12, 12, 12, 12, 18, 18, 12, 12, 2, 2, 2, 2, 8, 8, 2, 12, 12, 12, 12, 18, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012358 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471012358 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012358/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012358/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012358 Building ZINC001471012369 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012369' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012369 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471012369 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012369/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012369 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/528 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](C(F)F)CC1) `ZINC001471012369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471012369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471012369 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](C(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 15, 15, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 7, 2, 1, 1, 1, 1, 7, 9, 14, 14, 14, 14, 14, 14, 26, 26, 14, 14, 2, 2, 2, 2, 7, 7, 2, 14, 14, 14, 14, 26, 14, 14, 14, 14] 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012369 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012369/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012369 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 529) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/529 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/529' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](C(F)F)CC1) `ZINC001471012369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471012369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471012369 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](C(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 15, 15, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 6, 9, 14, 14, 14, 14, 14, 14, 22, 22, 14, 14, 2, 2, 2, 2, 5, 5, 2, 14, 14, 14, 14, 22, 14, 14, 14, 14] 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012369 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471012369 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012369/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012369/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012369 Building ZINC001471012369 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012369' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012369 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471012369 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012369/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012369 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 528) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/528: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](C(F)F)CC1) `ZINC001471012369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471012369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471012369 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](C(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 15, 15, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 7, 2, 1, 1, 1, 1, 7, 9, 14, 14, 14, 14, 14, 14, 26, 26, 14, 14, 2, 2, 2, 2, 7, 7, 2, 14, 14, 14, 14, 26, 14, 14, 14, 14] 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012369 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012369/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012369 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 529) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/529: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](C(F)F)CC1) `ZINC001471012369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471012369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471012369 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](C(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 15, 15, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 6, 9, 14, 14, 14, 14, 14, 14, 22, 22, 14, 14, 2, 2, 2, 2, 5, 5, 2, 14, 14, 14, 14, 22, 14, 14, 14, 14] 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012369 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471012369 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012369/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012369/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471012369 Building ZINC001471045101 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471045101' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471045101 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471045101 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471045101/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471045101 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/530 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C2CC2)CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001471045101.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471045101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471045101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001471045101 none COCC1(C2CC2)CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 13, 6, 6, 6, 14, 14, 6, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 6, 18, 18, 18, 13, 13, 14, 14, 14, 14, 14, 6, 6, 2, 5, 5, 2, 2, 2, 2, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 91 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471045101 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471045101/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471045101 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 531) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/531 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/531' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C2CC2)CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001471045101.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471045101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471045101/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001471045101 none COCC1(C2CC2)CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 5, 5, 5, 12, 12, 5, 2, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 5, 14, 14, 14, 10, 10, 12, 12, 12, 12, 12, 5, 5, 2, 7, 7, 2, 2, 2, 2, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 86 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471045101 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471045101 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471045101/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471045101/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471045101 Building ZINC001471045101 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471045101' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471045101 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471045101 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471045101/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471045101 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 530) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/530: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C2CC2)CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001471045101.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471045101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471045101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001471045101 none COCC1(C2CC2)CN(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 13, 6, 6, 6, 14, 14, 6, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 6, 18, 18, 18, 13, 13, 14, 14, 14, 14, 14, 6, 6, 2, 5, 5, 2, 2, 2, 2, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 91 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471045101 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471045101/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471045101 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 531) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/531: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C2CC2)CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001471045101.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471045101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471045101/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC001471045101 none COCC1(C2CC2)CN(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 5, 5, 5, 12, 12, 5, 2, 1, 2, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 5, 14, 14, 14, 10, 10, 12, 12, 12, 12, 12, 5, 5, 2, 7, 7, 2, 2, 2, 2, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 86 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471045101 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471045101 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471045101/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471045101/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471045101 Building ZINC001471214785 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471214785 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/532 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1) `ZINC001471214785.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471214785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214785 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 3, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 8, 8, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 533) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/533 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/533' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1) `ZINC001471214785.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471214785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214785 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 11, 3, 1, 1, 1, 2, 5, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 11, 11, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 534) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/534 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/534' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1) `ZINC001471214785.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471214785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214785 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 3, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 8, 8, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 535) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/535 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/535' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1) `ZINC001471214785.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471214785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214785 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 11, 3, 1, 1, 1, 2, 5, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 11, 11, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471214785 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 Building ZINC001471214785 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471214785 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 532) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/532: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1) `ZINC001471214785.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471214785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214785 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 3, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 8, 8, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 533) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/533: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1) `ZINC001471214785.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471214785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214785 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 11, 3, 1, 1, 1, 2, 5, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 11, 11, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 534) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/534: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1) `ZINC001471214785.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471214785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214785 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 3, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 8, 8, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 535) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/535: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1) `ZINC001471214785.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471214785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214785 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 11, 3, 1, 1, 1, 2, 5, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 11, 11, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471214785 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 Building ZINC001471214785 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471214785 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 532) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/532: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1) `ZINC001471214785.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471214785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214785 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 3, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 8, 8, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 533) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/533: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1) `ZINC001471214785.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471214785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214785 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 11, 3, 1, 1, 1, 2, 5, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 11, 11, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 534) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/534: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1) `ZINC001471214785.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471214785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214785 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 3, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 8, 8, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 535) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/535: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1) `ZINC001471214785.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471214785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214785 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 11, 3, 1, 1, 1, 2, 5, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 11, 11, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471214785 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 Building ZINC001471214785 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471214785 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 532) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/532: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1) `ZINC001471214785.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471214785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214785 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 3, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 8, 8, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 533) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/533: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1) `ZINC001471214785.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471214785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214785 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 11, 3, 1, 1, 1, 2, 5, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 11, 11, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 534) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/534: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1) `ZINC001471214785.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471214785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214785 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 3, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 8, 8, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 535) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/535: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1) `ZINC001471214785.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471214785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214785 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 11, 3, 1, 1, 1, 2, 5, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 11, 11, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471214785 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214785 Building ZINC001471214830 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471214830 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/536 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1) `ZINC001471214830.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471214830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214830 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 18, 18, 5, 1, 1, 1, 2, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 18, 18, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 537) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/537 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/537' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1) `ZINC001471214830.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471214830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214830 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 16, 16, 6, 1, 1, 1, 2, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 16, 16, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 71 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 538) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/538 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/538' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1) `ZINC001471214830.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471214830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214830 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 18, 18, 5, 1, 1, 1, 2, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 18, 18, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 539) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/539 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/539' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1) `ZINC001471214830.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471214830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214830 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 16, 16, 6, 1, 1, 1, 2, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 16, 16, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 71 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471214830 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 Building ZINC001471214830 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471214830 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 536) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/536: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1) `ZINC001471214830.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471214830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214830 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 18, 18, 5, 1, 1, 1, 2, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 18, 18, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 537) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/537: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1) `ZINC001471214830.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471214830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214830 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 16, 16, 6, 1, 1, 1, 2, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 16, 16, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 71 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 538) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/538: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1) `ZINC001471214830.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471214830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214830 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 18, 18, 5, 1, 1, 1, 2, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 18, 18, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 539) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/539: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1) `ZINC001471214830.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471214830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214830 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 16, 16, 6, 1, 1, 1, 2, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 16, 16, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 71 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471214830 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 Building ZINC001471214830 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471214830 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 536) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/536: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1) `ZINC001471214830.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471214830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214830 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 18, 18, 5, 1, 1, 1, 2, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 18, 18, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 537) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/537: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1) `ZINC001471214830.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471214830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214830 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 16, 16, 6, 1, 1, 1, 2, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 16, 16, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 71 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 538) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/538: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1) `ZINC001471214830.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471214830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214830 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 18, 18, 5, 1, 1, 1, 2, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 18, 18, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 539) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/539: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1) `ZINC001471214830.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471214830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214830 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 16, 16, 6, 1, 1, 1, 2, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 16, 16, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 71 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471214830 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 Building ZINC001471214830 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471214830 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 536) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/536: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1) `ZINC001471214830.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471214830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214830 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 18, 18, 5, 1, 1, 1, 2, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 18, 18, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 537) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/537: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1) `ZINC001471214830.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471214830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214830 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 16, 16, 6, 1, 1, 1, 2, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 16, 16, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 71 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 538) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/538: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1) `ZINC001471214830.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471214830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214830 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 18, 18, 5, 1, 1, 1, 2, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 18, 18, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 539) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/539: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1) `ZINC001471214830.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471214830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214830 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 16, 16, 6, 1, 1, 1, 2, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 16, 16, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 71 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471214830 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214830 Building ZINC001471214831 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471214831 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/540 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1) `ZINC001471214831.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471214831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214831 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 10, 3, 1, 1, 1, 2, 5, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 10, 10, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 541) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/541 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/541' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1) `ZINC001471214831.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471214831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214831 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 3, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 8, 8, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 542) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/542 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/542' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1) `ZINC001471214831.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471214831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214831 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 10, 3, 1, 1, 1, 2, 5, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 10, 10, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 543) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/543 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/543' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1) `ZINC001471214831.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471214831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214831 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 3, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 8, 8, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471214831 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 Building ZINC001471214831 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471214831 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 540) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/540: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1) `ZINC001471214831.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471214831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214831 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 10, 3, 1, 1, 1, 2, 5, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 10, 10, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 541) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/541: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1) `ZINC001471214831.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471214831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214831 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 3, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 8, 8, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 542) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/542: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1) `ZINC001471214831.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471214831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214831 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 10, 3, 1, 1, 1, 2, 5, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 10, 10, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 543) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/543: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1) `ZINC001471214831.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471214831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214831 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 3, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 8, 8, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471214831 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 Building ZINC001471214831 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471214831 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 540) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/540: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1) `ZINC001471214831.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471214831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214831 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 10, 3, 1, 1, 1, 2, 5, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 10, 10, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 541) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/541: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1) `ZINC001471214831.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471214831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214831 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 3, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 8, 8, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 542) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/542: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1) `ZINC001471214831.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471214831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214831 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 10, 3, 1, 1, 1, 2, 5, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 10, 10, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 543) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/543: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1) `ZINC001471214831.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471214831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214831 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 3, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 8, 8, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471214831 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 Building ZINC001471214831 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471214831 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 540) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/540: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1) `ZINC001471214831.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471214831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214831 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 10, 3, 1, 1, 1, 2, 5, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 10, 10, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 541) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/541: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1) `ZINC001471214831.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471214831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214831 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 3, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 8, 8, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 542) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/542: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1) `ZINC001471214831.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471214831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214831 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 10, 3, 1, 1, 1, 2, 5, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 10, 10, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 543) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/543: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1) `ZINC001471214831.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471214831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214831 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 2, 1, 1, 1, 2, 3, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 8, 8, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471214831 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214831 Building ZINC001471214832 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471214832 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/544 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1) `ZINC001471214832.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471214832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214832 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 5, 1, 1, 1, 2, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 15, 15, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 68 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 545) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/545 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/545' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1) `ZINC001471214832.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471214832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214832 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 5, 1, 1, 1, 2, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 15, 15, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 546) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/546 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/546' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1) `ZINC001471214832.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471214832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214832 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 5, 1, 1, 1, 2, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 15, 15, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 68 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 547) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/547 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/547' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1) `ZINC001471214832.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471214832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214832 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 5, 1, 1, 1, 2, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 15, 15, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471214832 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 Building ZINC001471214832 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471214832 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 544) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/544: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1) `ZINC001471214832.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471214832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214832 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 5, 1, 1, 1, 2, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 15, 15, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 68 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 545) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/545: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1) `ZINC001471214832.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471214832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214832 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 5, 1, 1, 1, 2, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 15, 15, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 546) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/546: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1) `ZINC001471214832.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471214832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214832 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 5, 1, 1, 1, 2, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 15, 15, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 68 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 547) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/547: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1) `ZINC001471214832.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471214832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214832 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 5, 1, 1, 1, 2, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 15, 15, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471214832 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 Building ZINC001471214832 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471214832 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 544) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/544: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1) `ZINC001471214832.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471214832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214832 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 5, 1, 1, 1, 2, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 15, 15, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 68 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 545) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/545: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1) `ZINC001471214832.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471214832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214832 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 5, 1, 1, 1, 2, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 15, 15, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 546) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/546: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1) `ZINC001471214832.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471214832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214832 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 5, 1, 1, 1, 2, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 15, 15, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 68 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 547) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/547: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1) `ZINC001471214832.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471214832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214832 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 5, 1, 1, 1, 2, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 15, 15, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471214832 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 Building ZINC001471214832 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471214832 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 544) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/544: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1) `ZINC001471214832.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471214832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214832 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 5, 1, 1, 1, 2, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 15, 15, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 68 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 545) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/545: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1) `ZINC001471214832.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471214832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214832 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 5, 1, 1, 1, 2, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 15, 15, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 546) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/546: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1) `ZINC001471214832.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471214832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214832 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 5, 1, 1, 1, 2, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 15, 15, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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]) total number of confs: 68 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 547) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/547: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1) `ZINC001471214832.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471214832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001471214832 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H]2[C@H](CCN2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 5, 1, 1, 1, 2, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 15, 15, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471214832 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471214832 Building ZINC001471527127 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527127' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527127 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471527127 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527127/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527127 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/548 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1Cn2nccc2N(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001471527127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471527127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001471527127 none C[C@H]1Cn2nccc2N(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 2, 8, 1, 1, 1, 5, 5, 5, 16, 16, 16, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 5, 16, 16, 5, 5, 5, 5, 10, 10] 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: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527127 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527127/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527127 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 549) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/549 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/549' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1Cn2nccc2N(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001471527127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471527127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001471527127 none C[C@H]1Cn2nccc2N(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 1, 6, 1, 1, 1, 4, 4, 4, 15, 15, 15, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 4, 15, 15, 4, 4, 4, 4, 8, 8] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527127 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471527127 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527127/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527127/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527127 Building ZINC001471527127 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527127' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527127 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471527127 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527127/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527127 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 548) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/548: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1Cn2nccc2N(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001471527127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471527127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001471527127 none C[C@H]1Cn2nccc2N(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 2, 8, 1, 1, 1, 5, 5, 5, 16, 16, 16, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 5, 16, 16, 5, 5, 5, 5, 10, 10] 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: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527127 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527127/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527127 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 549) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/549: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1Cn2nccc2N(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001471527127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471527127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001471527127 none C[C@H]1Cn2nccc2N(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 1, 6, 1, 1, 1, 4, 4, 4, 15, 15, 15, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 4, 15, 15, 4, 4, 4, 4, 8, 8] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527127 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471527127 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527127/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527127/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527127 Building ZINC001471527129 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527129' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527129 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471527129 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527129/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527129 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/550 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1Cn2nccc2N(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001471527129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471527129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001471527129 none C[C@@H]1Cn2nccc2N(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 1, 6, 1, 1, 1, 5, 5, 5, 16, 16, 16, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 5, 16, 16, 5, 5, 5, 5, 9, 9] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527129 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527129/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527129 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 551) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/551 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/551' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1Cn2nccc2N(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001471527129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471527129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001471527129 none C[C@@H]1Cn2nccc2N(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 2, 8, 1, 1, 1, 5, 5, 5, 16, 16, 16, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 5, 16, 16, 5, 5, 5, 5, 10, 10] 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: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527129 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471527129 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527129/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527129/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527129 Building ZINC001471527129 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527129' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527129 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471527129 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527129/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527129 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 550) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/550: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1Cn2nccc2N(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001471527129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471527129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001471527129 none C[C@@H]1Cn2nccc2N(C(=O)[C@@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 1, 6, 1, 1, 1, 5, 5, 5, 16, 16, 16, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 5, 16, 16, 5, 5, 5, 5, 9, 9] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527129 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527129/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527129 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 551) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/551: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1Cn2nccc2N(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1) `ZINC001471527129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471527129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001471527129 none C[C@@H]1Cn2nccc2N(C(=O)[C@]([O-])([SiH3])c2cc(S(N)(=O)=O)cn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 2, 8, 1, 1, 1, 5, 5, 5, 16, 16, 16, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 5, 16, 16, 5, 5, 5, 5, 10, 10] 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: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527129 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471527129 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527129/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527129/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471527129 Building ZINC001471565786 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565786' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565786 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471565786 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565786/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565786 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/552 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1COCC[C@@H]1N(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001471565786.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471565786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471565786 none CO[C@@H]1COCC[C@@H]1N(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 5, 7, 5, 12, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 5, 11, 4, 6, 1, 4, 1, 1, 1, 4, 4, 4, 15, 15, 15, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 4, 15, 15, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 87 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565786 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565786/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565786 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 553) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/553 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/553' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1COCC[C@@H]1N(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001471565786.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471565786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471565786 none CO[C@@H]1COCC[C@@H]1N(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 5, 7, 5, 12, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 5, 11, 2, 5, 1, 2, 1, 1, 1, 3, 3, 3, 10, 10, 10, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 3, 10, 10, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565786 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471565786 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565786/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565786/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565786 Building ZINC001471565786 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565786' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565786 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471565786 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565786/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565786 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 552) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/552: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1COCC[C@@H]1N(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001471565786.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471565786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471565786 none CO[C@@H]1COCC[C@@H]1N(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 5, 7, 5, 12, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 5, 11, 4, 6, 1, 4, 1, 1, 1, 4, 4, 4, 15, 15, 15, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 4, 15, 15, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 87 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565786 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565786/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565786 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 553) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/553: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1COCC[C@@H]1N(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001471565786.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471565786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471565786 none CO[C@@H]1COCC[C@@H]1N(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 5, 7, 5, 12, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 5, 11, 2, 5, 1, 2, 1, 1, 1, 3, 3, 3, 10, 10, 10, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 3, 10, 10, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565786 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471565786 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565786/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565786/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565786 Building ZINC001471565787 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565787' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565787 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471565787 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565787/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565787 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/554 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1COCC[C@@H]1N(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001471565787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471565787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471565787 none CO[C@H]1COCC[C@@H]1N(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 5, 7, 5, 12, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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: [17, 17, 17, 17, 17, 17, 17, 17, 5, 17, 2, 4, 1, 2, 1, 1, 1, 3, 3, 3, 9, 9, 9, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 4, 4, 3, 9, 9, 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]) total number of confs: 71 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565787 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565787/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565787 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 555) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/555 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/555' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1COCC[C@@H]1N(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001471565787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471565787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471565787 none CO[C@H]1COCC[C@@H]1N(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 5, 7, 5, 12, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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: [22, 19, 19, 19, 19, 19, 19, 19, 6, 19, 3, 5, 1, 3, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 22, 22, 22, 19, 19, 19, 19, 19, 19, 5, 5, 5, 2, 7, 7, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 79 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565787 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471565787 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565787/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565787/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565787 Building ZINC001471565787 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565787' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565787 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471565787 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565787/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565787 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 554) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/554: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1COCC[C@@H]1N(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001471565787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471565787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471565787 none CO[C@H]1COCC[C@@H]1N(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 5, 7, 5, 12, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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: [17, 17, 17, 17, 17, 17, 17, 17, 5, 17, 2, 4, 1, 2, 1, 1, 1, 3, 3, 3, 9, 9, 9, 3, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 4, 4, 3, 9, 9, 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]) total number of confs: 71 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565787 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565787/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565787 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 555) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1COCC[C@@H]1N(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001471565787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471565787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471565787 none CO[C@H]1COCC[C@@H]1N(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 5, 7, 5, 12, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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: [22, 19, 19, 19, 19, 19, 19, 19, 6, 19, 3, 5, 1, 3, 1, 1, 1, 2, 2, 2, 7, 7, 7, 2, 2, 2, 22, 22, 22, 19, 19, 19, 19, 19, 19, 5, 5, 5, 2, 7, 7, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 79 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565787 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471565787 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565787/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565787/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565787 Building ZINC001471565788 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565788' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565788 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471565788 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565788/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565788 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/556 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1COCC[C@H]1N(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001471565788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471565788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471565788 none CO[C@H]1COCC[C@H]1N(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 5, 7, 5, 12, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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: [10, 10, 10, 10, 10, 10, 10, 10, 5, 10, 2, 5, 1, 2, 1, 1, 1, 3, 3, 3, 12, 12, 12, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 3, 12, 12, 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565788 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565788/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565788 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 557) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/557 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/557' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1COCC[C@H]1N(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001471565788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471565788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471565788 none CO[C@H]1COCC[C@H]1N(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 5, 7, 5, 12, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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: [12, 11, 11, 11, 11, 11, 11, 11, 4, 11, 4, 6, 1, 4, 1, 1, 1, 5, 5, 5, 17, 17, 17, 5, 5, 5, 12, 12, 12, 11, 11, 11, 11, 11, 11, 6, 6, 6, 5, 17, 17, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 97 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565788 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471565788 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565788/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565788/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565788 Building ZINC001471565788 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565788' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565788 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471565788 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565788/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565788 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 556) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1COCC[C@H]1N(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001471565788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471565788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471565788 none CO[C@H]1COCC[C@H]1N(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 5, 7, 5, 12, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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: [10, 10, 10, 10, 10, 10, 10, 10, 5, 10, 2, 5, 1, 2, 1, 1, 1, 3, 3, 3, 12, 12, 12, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 3, 12, 12, 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565788 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565788/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565788 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 557) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/557: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1COCC[C@H]1N(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001471565788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471565788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471565788 none CO[C@H]1COCC[C@H]1N(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 5, 7, 5, 12, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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: [12, 11, 11, 11, 11, 11, 11, 11, 4, 11, 4, 6, 1, 4, 1, 1, 1, 5, 5, 5, 17, 17, 17, 5, 5, 5, 12, 12, 12, 11, 11, 11, 11, 11, 11, 6, 6, 6, 5, 17, 17, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 97 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565788 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471565788 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565788/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565788/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565788 Building ZINC001471565789 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565789' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565789 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471565789 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565789/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565789 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/558 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1COCC[C@H]1N(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001471565789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471565789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471565789 none CO[C@@H]1COCC[C@H]1N(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 5, 7, 5, 12, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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: [19, 17, 17, 17, 17, 17, 17, 17, 7, 17, 3, 4, 1, 3, 1, 1, 1, 2, 2, 2, 6, 6, 6, 2, 2, 2, 19, 19, 19, 17, 17, 17, 17, 17, 17, 4, 4, 4, 2, 6, 6, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 64 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565789 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565789/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565789 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 559) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/559 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/559' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1COCC[C@H]1N(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001471565789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471565789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471565789 none CO[C@@H]1COCC[C@H]1N(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 5, 7, 5, 12, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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: [16, 16, 16, 16, 16, 16, 16, 16, 6, 16, 2, 4, 1, 2, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 2, 8, 8, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 69 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565789 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471565789 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565789/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565789/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565789 Building ZINC001471565789 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565789' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565789 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471565789 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565789/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565789 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 558) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/558: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1COCC[C@H]1N(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001471565789.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471565789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471565789 none CO[C@@H]1COCC[C@H]1N(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 5, 7, 5, 12, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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: [19, 17, 17, 17, 17, 17, 17, 17, 7, 17, 3, 4, 1, 3, 1, 1, 1, 2, 2, 2, 6, 6, 6, 2, 2, 2, 19, 19, 19, 17, 17, 17, 17, 17, 17, 4, 4, 4, 2, 6, 6, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 64 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565789 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565789/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565789 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 559) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/559: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1COCC[C@H]1N(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001471565789.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471565789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565789/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471565789 none CO[C@@H]1COCC[C@H]1N(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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, 5, 7, 5, 12, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 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: [16, 16, 16, 16, 16, 16, 16, 16, 6, 16, 2, 4, 1, 2, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 2, 8, 8, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 69 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565789 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471565789 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565789/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565789/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471565789 Building ZINC001471703554 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471703554' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471703554 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471703554 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471703554/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471703554 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/560 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN(CC(=O)NC)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001471703554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471703554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471703554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001471703554 none CNC(=O)CN(CC(=O)NC)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 8, 5, 1, 11, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 9, 15, 4, 3, 4, 6, 16, 16, 16, 1, 3, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 15, 15, 15, 15, 9, 9, 6, 6, 16, 16, 16, 16, 6, 9, 9, 6, 9, 9, 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: 109 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471703554 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471703554/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471703554 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 561) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/561 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/561' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN(CC(=O)NC)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001471703554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471703554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471703554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001471703554 none CNC(=O)CN(CC(=O)NC)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 8, 5, 1, 11, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 14, 4, 3, 4, 6, 15, 15, 15, 1, 3, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 14, 14, 14, 14, 9, 9, 6, 6, 15, 15, 15, 15, 6, 10, 10, 10, 10, 10, 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: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471703554 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471703554 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471703554/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471703554/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471703554 Building ZINC001471703554 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471703554' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471703554 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471703554 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471703554/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471703554 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 560) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/560: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN(CC(=O)NC)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001471703554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471703554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471703554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001471703554 none CNC(=O)CN(CC(=O)NC)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 8, 5, 1, 11, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 9, 15, 4, 3, 4, 6, 16, 16, 16, 1, 3, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 15, 15, 15, 15, 9, 9, 6, 6, 16, 16, 16, 16, 6, 9, 9, 6, 9, 9, 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: 109 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471703554 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471703554/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471703554 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 561) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/561: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN(CC(=O)NC)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001471703554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471703554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471703554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001471703554 none CNC(=O)CN(CC(=O)NC)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 8, 5, 1, 11, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 14, 4, 3, 4, 6, 15, 15, 15, 1, 3, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 14, 14, 14, 14, 9, 9, 6, 6, 15, 15, 15, 15, 6, 10, 10, 10, 10, 10, 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: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471703554 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001471703554 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471703554/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471703554/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001471703554 Building ZINC001472039328 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472039328' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472039328 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472039328 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472039328/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472039328 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/562 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@]12C[C@H]1COC21CCC1) `ZINC001472039328.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472039328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472039328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001472039328 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@]12C[C@H]1COC21CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [7, 7, 7, 7, 7, 23, 23, 23, 7, 1, 1, 1, 1, 7, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 7, 7, 7, 7, 23, 23, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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, 42]) total number of confs: 94 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472039328 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472039328/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472039328 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 563) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/563 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/563' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@]12C[C@H]1COC21CCC1) `ZINC001472039328.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472039328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472039328/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001472039328 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@]12C[C@H]1COC21CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [4, 4, 4, 4, 4, 15, 15, 15, 4, 1, 1, 1, 1, 7, 7, 7, 11, 9, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 4, 15, 15, 4, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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, 42]) total number of confs: 80 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472039328 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001472039328 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472039328/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472039328/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472039328 Building ZINC001472039328 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472039328' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472039328 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472039328 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472039328/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472039328 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 562) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/562: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@]12C[C@H]1COC21CCC1) `ZINC001472039328.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472039328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472039328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001472039328 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N[C@]12C[C@H]1COC21CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [7, 7, 7, 7, 7, 23, 23, 23, 7, 1, 1, 1, 1, 7, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 7, 7, 7, 7, 23, 23, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 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, 42]) total number of confs: 94 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472039328 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472039328/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472039328 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 563) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/563: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@]12C[C@H]1COC21CCC1) `ZINC001472039328.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472039328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472039328/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001472039328 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N[C@]12C[C@H]1COC21CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', '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, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [4, 4, 4, 4, 4, 15, 15, 15, 4, 1, 1, 1, 1, 7, 7, 7, 11, 9, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 4, 15, 15, 4, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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, 42]) total number of confs: 80 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472039328 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001472039328 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472039328/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472039328/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472039328 Building ZINC001472054688 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054688' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054688 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472054688 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054688/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054688 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/564 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](c2ncccn2)C1) `ZINC001472054688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472054688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001472054688 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](c2ncccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 2, 3, 9, 9, 9, 9, 9, 21, 21, 14, 21, 21, 9, 2, 2, 2, 2, 5, 5, 2, 9, 9, 9, 9, 21, 17, 21, 9, 9] 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: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054688 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054688/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054688 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 565) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/565 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/565' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](c2ncccn2)C1) `ZINC001472054688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472054688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001472054688 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](c2ncccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 2, 1, 1, 1, 1, 2, 4, 9, 9, 9, 9, 9, 19, 19, 11, 19, 19, 9, 2, 2, 2, 2, 7, 7, 2, 9, 9, 9, 9, 19, 14, 19, 9, 9] 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: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054688 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001472054688 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054688/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054688/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054688 Building ZINC001472054688 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054688' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054688 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472054688 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054688/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054688 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 564) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/564: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](c2ncccn2)C1) `ZINC001472054688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472054688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001472054688 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](c2ncccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 2, 3, 9, 9, 9, 9, 9, 21, 21, 14, 21, 21, 9, 2, 2, 2, 2, 5, 5, 2, 9, 9, 9, 9, 21, 17, 21, 9, 9] 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: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054688 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054688/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054688 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 565) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/565: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](c2ncccn2)C1) `ZINC001472054688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472054688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001472054688 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](c2ncccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 2, 1, 1, 1, 1, 2, 4, 9, 9, 9, 9, 9, 19, 19, 11, 19, 19, 9, 2, 2, 2, 2, 7, 7, 2, 9, 9, 9, 9, 19, 14, 19, 9, 9] 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: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054688 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001472054688 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054688/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054688/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054688 Building ZINC001472054689 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054689' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054689 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472054689 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054689/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054689 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/566 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](c2ncccn2)C1) `ZINC001472054689.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472054689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001472054689 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](c2ncccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 2, 1, 1, 1, 1, 2, 3, 9, 9, 9, 9, 9, 20, 20, 9, 20, 20, 9, 2, 2, 2, 2, 7, 7, 2, 9, 9, 9, 9, 20, 9, 20, 9, 9] 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054689 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054689/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054689 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 567) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/567 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/567' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](c2ncccn2)C1) `ZINC001472054689.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472054689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054689/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001472054689 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](c2ncccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 2, 1, 1, 1, 1, 2, 3, 9, 9, 9, 9, 9, 21, 21, 12, 21, 21, 9, 2, 2, 2, 2, 7, 7, 2, 9, 9, 9, 9, 21, 12, 21, 9, 9] 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: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054689 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001472054689 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054689/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054689/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054689 Building ZINC001472054689 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054689' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054689 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472054689 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054689/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054689 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 566) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/566: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](c2ncccn2)C1) `ZINC001472054689.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472054689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001472054689 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](c2ncccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 2, 1, 1, 1, 1, 2, 3, 9, 9, 9, 9, 9, 20, 20, 9, 20, 20, 9, 2, 2, 2, 2, 7, 7, 2, 9, 9, 9, 9, 20, 9, 20, 9, 9] 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054689 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054689/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054689 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 567) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/567: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](c2ncccn2)C1) `ZINC001472054689.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472054689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054689/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001472054689 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](c2ncccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'N.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'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 7, 7, 2, 1, 1, 1, 1, 2, 3, 9, 9, 9, 9, 9, 21, 21, 12, 21, 21, 9, 2, 2, 2, 2, 7, 7, 2, 9, 9, 9, 9, 21, 12, 21, 9, 9] 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: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054689 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001472054689 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054689/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054689/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472054689 Building ZINC001472073134 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073134' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073134 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472073134 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073134/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073134 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/568 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](C)C(=O)OC) `ZINC001472073134.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472073134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001472073134 none CCCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](C)C(=O)OC 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens 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, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 4, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 8, 8, 2, 2, 2, 2, 6, 6, 6, 9, 9, 9] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 85 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073134 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073134/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073134 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 569) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/569 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/569' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](C)C(=O)OC) `ZINC001472073134.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472073134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073134/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001472073134 none CCCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](C)C(=O)OC 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 4, 6, 6, 6, 11, 11, 11, 7, 7, 7, 7, 7, 7, 7, 2, 5, 5, 2, 2, 2, 2, 6, 6, 6, 11, 11, 11] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 74 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073134 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001472073134 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073134/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073134/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073134 Building ZINC001472073134 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073134' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073134 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472073134 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073134/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073134 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 568) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/568: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](C)C(=O)OC) `ZINC001472073134.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472073134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001472073134 none CCCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](C)C(=O)OC 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens 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, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 4, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 8, 8, 2, 2, 2, 2, 6, 6, 6, 9, 9, 9] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 85 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073134 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073134/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073134 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 569) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/569: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](C)C(=O)OC) `ZINC001472073134.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472073134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073134/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001472073134 none CCCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@H](C)C(=O)OC 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 4, 6, 6, 6, 11, 11, 11, 7, 7, 7, 7, 7, 7, 7, 2, 5, 5, 2, 2, 2, 2, 6, 6, 6, 11, 11, 11] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 74 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073134 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001472073134 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073134/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073134/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073134 Building ZINC001472073135 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073135' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073135 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472073135 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073135/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073135 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/570 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](C)C(=O)OC) `ZINC001472073135.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472073135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001472073135 none CCCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](C)C(=O)OC 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 4, 6, 6, 6, 11, 11, 11, 7, 7, 7, 7, 7, 7, 7, 2, 5, 5, 2, 2, 2, 2, 6, 6, 6, 11, 11, 11] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 74 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073135 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073135/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073135 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 571) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/571 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/571' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](C)C(=O)OC) `ZINC001472073135.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472073135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073135/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001472073135 none CCCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](C)C(=O)OC 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 4, 6, 6, 6, 9, 9, 9, 8, 8, 8, 8, 8, 8, 8, 2, 8, 8, 2, 2, 2, 2, 6, 6, 6, 9, 9, 9] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 79 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073135 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001472073135 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073135/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073135/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073135 Building ZINC001472073135 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073135' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073135 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472073135 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073135/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073135 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 570) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/570: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](C)C(=O)OC) `ZINC001472073135.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472073135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001472073135 none CCCN(C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](C)C(=O)OC 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 5, 5, 2, 2, 2, 4, 6, 6, 6, 11, 11, 11, 7, 7, 7, 7, 7, 7, 7, 2, 5, 5, 2, 2, 2, 2, 6, 6, 6, 11, 11, 11] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 74 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073135 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073135/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073135 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 571) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/571: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](C)C(=O)OC) `ZINC001472073135.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472073135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073135/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001472073135 none CCCN(C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C)[C@@H](C)C(=O)OC 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', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 5, 7, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 8, 8, 8, 2, 2, 2, 4, 6, 6, 6, 9, 9, 9, 8, 8, 8, 8, 8, 8, 8, 2, 8, 8, 2, 2, 2, 2, 6, 6, 6, 9, 9, 9] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 79 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073135 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001472073135 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073135/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073135/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472073135 Building ZINC001472082665 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472082665' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472082665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472082665 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472082665/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472082665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/572 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1nc(CS(C)(=O)=O)n[nH]1) `ZINC001472082665.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472082665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472082665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001472082665 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1nc(CS(C)(=O)=O)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 5, 14, 5, 11, 11, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 13, 13, 13, 33, 50, 50, 50, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 3, 7, 7, 33, 33, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472082665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472082665/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472082665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 573) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/573 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/573' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1nc(CS(C)(=O)=O)n[nH]1) `ZINC001472082665.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472082665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472082665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001472082665 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1nc(CS(C)(=O)=O)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 5, 14, 5, 11, 11, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 13, 13, 13, 33, 50, 50, 50, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 3, 7, 7, 33, 33, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472082665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001472082665 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472082665/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472082665/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472082665 Building ZINC001472082665 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472082665' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472082665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472082665 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472082665/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472082665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 572) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/572: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1nc(CS(C)(=O)=O)n[nH]1) `ZINC001472082665.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472082665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472082665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001472082665 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1nc(CS(C)(=O)=O)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 5, 14, 5, 11, 11, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 13, 13, 13, 33, 50, 50, 50, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 3, 7, 7, 33, 33, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472082665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472082665/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472082665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 573) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/573: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1nc(CS(C)(=O)=O)n[nH]1) `ZINC001472082665.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472082665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472082665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001472082665 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1nc(CS(C)(=O)=O)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 5, 14, 5, 11, 11, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 13, 13, 13, 33, 50, 50, 50, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 3, 7, 7, 33, 33, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472082665 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001472082665 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472082665/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472082665/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472082665 Building ZINC001472252734 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472252734' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472252734 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472252734 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472252734/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472252734 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/574 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@]12C[C@H]1COC21CCC1) `ZINC001472252734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472252734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472252734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001472252734 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@]12C[C@H]1COC21CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 3, 1, 1, 1, 1, 2, 2, 2, 13, 21, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 6, 6, 3, 2, 13, 13, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 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, 42, 43, 44, 45]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472252734 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472252734/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472252734 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 575) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/575 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/575' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@]12C[C@H]1COC21CCC1) `ZINC001472252734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472252734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472252734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001472252734 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@]12C[C@H]1COC21CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 2, 2, 2, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 2, 2, 2, 2, 5, 5, 2, 2, 12, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 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, 42, 43, 44, 45]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472252734 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001472252734 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472252734/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472252734/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472252734 Building ZINC001472252734 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472252734' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472252734 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472252734 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472252734/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472252734 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 574) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/574: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@]12C[C@H]1COC21CCC1) `ZINC001472252734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472252734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472252734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001472252734 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)NC[C@]12C[C@H]1COC21CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in 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, 3, 1, 1, 1, 1, 2, 2, 2, 13, 21, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 6, 6, 3, 2, 13, 13, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 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, 42, 43, 44, 45]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472252734 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472252734/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472252734 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 575) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/575: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@]12C[C@H]1COC21CCC1) `ZINC001472252734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472252734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472252734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001472252734 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)NC[C@]12C[C@H]1COC21CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 5, 2, 1, 1, 1, 1, 2, 2, 2, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 2, 2, 2, 2, 5, 5, 2, 2, 12, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 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, 42, 43, 44, 45]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472252734 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001472252734 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472252734/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472252734/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472252734 Building ZINC001472269591 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269591' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269591 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472269591 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269591/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269591 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/576 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@]1(C)C1CC1) `ZINC001472269591.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472269591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001472269591 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@]1(C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [5, 5, 5, 5, 5, 18, 18, 18, 5, 1, 1, 1, 2, 6, 8, 10, 10, 10, 10, 10, 10, 10, 13, 13, 5, 5, 5, 5, 18, 18, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 90 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269591 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269591/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269591 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 577) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/577 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/577' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@]1(C)C1CC1) `ZINC001472269591.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472269591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269591/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001472269591 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@]1(C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [3, 3, 3, 3, 3, 11, 11, 11, 3, 1, 1, 1, 2, 7, 9, 10, 10, 10, 10, 10, 10, 10, 12, 12, 3, 3, 3, 3, 11, 11, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 65 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269591 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001472269591 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269591/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269591/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269591 Building ZINC001472269591 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269591' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269591 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472269591 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269591/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269591 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 576) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/576: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@]1(C)C1CC1) `ZINC001472269591.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472269591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001472269591 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@]1(C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [5, 5, 5, 5, 5, 18, 18, 18, 5, 1, 1, 1, 2, 6, 8, 10, 10, 10, 10, 10, 10, 10, 13, 13, 5, 5, 5, 5, 18, 18, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 90 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269591 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269591/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269591 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 577) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/577: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@]1(C)C1CC1) `ZINC001472269591.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472269591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269591/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001472269591 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@]1(C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [3, 3, 3, 3, 3, 11, 11, 11, 3, 1, 1, 1, 2, 7, 9, 10, 10, 10, 10, 10, 10, 10, 12, 12, 3, 3, 3, 3, 11, 11, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 65 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269591 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001472269591 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269591/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269591/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269591 Building ZINC001472269592 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269592' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269592 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472269592 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269592/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269592 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/578 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@]1(C)C1CC1) `ZINC001472269592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472269592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001472269592 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@]1(C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [4, 4, 4, 4, 4, 13, 13, 13, 4, 1, 1, 1, 2, 6, 8, 10, 10, 10, 10, 10, 10, 10, 12, 12, 4, 4, 4, 4, 13, 13, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 72 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269592 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269592/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269592 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 579) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/579 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/579' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@]1(C)C1CC1) `ZINC001472269592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472269592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001472269592 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@]1(C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [4, 4, 4, 4, 4, 15, 15, 15, 4, 1, 1, 1, 2, 6, 8, 8, 8, 8, 8, 8, 8, 8, 11, 11, 4, 4, 4, 4, 15, 15, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 78 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269592 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001472269592 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269592/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269592/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269592 Building ZINC001472269592 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269592' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269592 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472269592 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269592/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269592 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 578) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/578: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@]1(C)C1CC1) `ZINC001472269592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472269592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001472269592 none Cn1cc(S(N)(=O)=O)cc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@]1(C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [4, 4, 4, 4, 4, 13, 13, 13, 4, 1, 1, 1, 2, 6, 8, 10, 10, 10, 10, 10, 10, 10, 12, 12, 4, 4, 4, 4, 13, 13, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 72 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269592 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269592/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269592 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 579) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/579: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@]1(C)C1CC1) `ZINC001472269592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472269592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001472269592 none Cn1cc(S(N)(=O)=O)cc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@]1(C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 8, 11, 11, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 6, 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: [4, 4, 4, 4, 4, 15, 15, 15, 4, 1, 1, 1, 2, 6, 8, 8, 8, 8, 8, 8, 8, 8, 11, 11, 4, 4, 4, 4, 15, 15, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 78 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269592 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001472269592 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269592/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269592/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001472269592 Building ZINC001479500845 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479500845' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479500845 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001479500845 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479500845/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479500845 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/580 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](O)CN[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1c1cnn(C)c1) `ZINC001479500845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479500845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479500845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001479500845 none COC[C@H](O)CN[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 27, 20, 13, 20, 20, 7, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 16, 16, 16, 16, 16, 32, 32, 32, 27, 27, 60, 13, 13, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 16, 16, 16, 16, 16] 150 rigid atoms, others: [48, 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, 39, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 214 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479500845 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479500845/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479500845 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 581) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/581 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/581' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](O)CN[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1c1cnn(C)c1) `ZINC001479500845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479500845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479500845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001479500845 none COC[C@H](O)CN[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 32, 29, 16, 29, 29, 9, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 17, 17, 17, 17, 17, 34, 34, 34, 32, 32, 87, 16, 16, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 17, 17, 17] 150 rigid atoms, others: [48, 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, 39, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 250 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479500845 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001479500845 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479500845/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479500845/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479500845 Building ZINC001479500845 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479500845' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479500845 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001479500845 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479500845/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479500845 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 580) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/580: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](O)CN[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1c1cnn(C)c1) `ZINC001479500845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479500845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479500845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001479500845 none COC[C@H](O)CN[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 27, 20, 13, 20, 20, 7, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 16, 16, 16, 16, 16, 32, 32, 32, 27, 27, 60, 13, 13, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 16, 16, 16, 16, 16] 150 rigid atoms, others: [48, 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, 39, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 214 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479500845 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479500845/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479500845 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 581) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/581: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](O)CN[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1c1cnn(C)c1) `ZINC001479500845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479500845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479500845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001479500845 none COC[C@H](O)CN[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 32, 29, 16, 29, 29, 9, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 17, 17, 17, 17, 17, 34, 34, 34, 32, 32, 87, 16, 16, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 17, 17, 17] 150 rigid atoms, others: [48, 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, 39, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 250 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479500845 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001479500845 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479500845/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479500845/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479500845 Building ZINC001479665247 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479665247 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/582 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/582' -> `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]2CCN(CCNS(C)(=O)=O)C[C@H]2C1) `ZINC001479665247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479665247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001479665247 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(CCNS(C)(=O)=O)C[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 9, 9, 9, 9, 9, 9, 9, 17, 23, 41, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 17, 17, 23, 23, 41, 49, 50, 50, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 204 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 583) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/583 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/583' -> `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]2CCN(CCNS(C)(=O)=O)C[C@H]2C1) `ZINC001479665247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479665247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001479665247 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(CCNS(C)(=O)=O)C[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 6, 6, 6, 6, 6, 6, 6, 13, 20, 41, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 13, 13, 20, 20, 41, 48, 50, 50, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 215 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 584) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/584 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/584' -> `2.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]2CCN(CCNS(C)(=O)=O)C[C@H]2C1) `ZINC001479665247.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479665247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001479665247 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(CCNS(C)(=O)=O)C[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 9, 9, 9, 9, 9, 9, 9, 17, 23, 41, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 17, 17, 23, 23, 41, 49, 50, 50, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 204 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 585) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/585 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/585' -> `3.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]2CCN(CCNS(C)(=O)=O)C[C@H]2C1) `ZINC001479665247.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479665247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001479665247 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(CCNS(C)(=O)=O)C[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 6, 6, 6, 6, 6, 6, 6, 13, 20, 41, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 13, 13, 20, 20, 41, 48, 50, 50, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 215 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001479665247 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 Building ZINC001479665247 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479665247 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 582) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/582: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(CCNS(C)(=O)=O)C[C@H]2C1) `ZINC001479665247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479665247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001479665247 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(CCNS(C)(=O)=O)C[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 9, 9, 9, 9, 9, 9, 9, 17, 23, 41, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 17, 17, 23, 23, 41, 49, 50, 50, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 204 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 583) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/583: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(CCNS(C)(=O)=O)C[C@H]2C1) `ZINC001479665247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479665247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001479665247 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(CCNS(C)(=O)=O)C[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 6, 6, 6, 6, 6, 6, 6, 13, 20, 41, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 13, 13, 20, 20, 41, 48, 50, 50, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 215 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 584) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/584: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]2CCN(CCNS(C)(=O)=O)C[C@H]2C1) `ZINC001479665247.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479665247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001479665247 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(CCNS(C)(=O)=O)C[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 9, 9, 9, 9, 9, 9, 9, 17, 23, 41, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 17, 17, 23, 23, 41, 49, 50, 50, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 204 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 585) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/585: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]2CCN(CCNS(C)(=O)=O)C[C@H]2C1) `ZINC001479665247.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479665247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001479665247 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(CCNS(C)(=O)=O)C[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 6, 6, 6, 6, 6, 6, 6, 13, 20, 41, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 13, 13, 20, 20, 41, 48, 50, 50, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 215 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001479665247 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 Building ZINC001479665247 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479665247 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 582) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/582: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(CCNS(C)(=O)=O)C[C@H]2C1) `ZINC001479665247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479665247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001479665247 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(CCNS(C)(=O)=O)C[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 9, 9, 9, 9, 9, 9, 9, 17, 23, 41, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 17, 17, 23, 23, 41, 49, 50, 50, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 204 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 583) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/583: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(CCNS(C)(=O)=O)C[C@H]2C1) `ZINC001479665247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479665247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001479665247 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(CCNS(C)(=O)=O)C[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 6, 6, 6, 6, 6, 6, 6, 13, 20, 41, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 13, 13, 20, 20, 41, 48, 50, 50, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 215 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 584) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/584: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]2CCN(CCNS(C)(=O)=O)C[C@H]2C1) `ZINC001479665247.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479665247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001479665247 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(CCNS(C)(=O)=O)C[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 9, 9, 9, 9, 9, 9, 9, 17, 23, 41, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 17, 17, 23, 23, 41, 49, 50, 50, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 204 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 585) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/585: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]2CCN(CCNS(C)(=O)=O)C[C@H]2C1) `ZINC001479665247.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479665247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001479665247 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(CCNS(C)(=O)=O)C[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 6, 6, 6, 6, 6, 6, 6, 13, 20, 41, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 13, 13, 20, 20, 41, 48, 50, 50, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 215 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001479665247 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 Building ZINC001479665247 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001479665247 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 582) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/582: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(CCNS(C)(=O)=O)C[C@H]2C1) `ZINC001479665247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001479665247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001479665247 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(CCNS(C)(=O)=O)C[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 9, 9, 9, 9, 9, 9, 9, 17, 23, 41, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 17, 17, 23, 23, 41, 49, 50, 50, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 204 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 583) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/583: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(CCNS(C)(=O)=O)C[C@H]2C1) `ZINC001479665247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001479665247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001479665247 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(CCNS(C)(=O)=O)C[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 6, 6, 6, 6, 6, 6, 6, 13, 20, 41, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 13, 13, 20, 20, 41, 48, 50, 50, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 215 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 584) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/584: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]2CCN(CCNS(C)(=O)=O)C[C@H]2C1) `ZINC001479665247.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001479665247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001479665247 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(CCNS(C)(=O)=O)C[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 7, 9, 9, 9, 9, 9, 9, 9, 17, 23, 41, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 17, 17, 23, 23, 41, 49, 50, 50, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 204 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 585) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/585: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=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]2CCN(CCNS(C)(=O)=O)C[C@H]2C1) `ZINC001479665247.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001479665247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001479665247 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CCN(CCNS(C)(=O)=O)C[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 6, 6, 6, 6, 6, 6, 6, 13, 20, 41, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 13, 13, 20, 20, 41, 48, 50, 50, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 215 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001479665247 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001479665247 Building ZINC001486527909 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001486527909' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001486527909 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001486527909 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001486527909/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001486527909 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/586 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@H]1C1CCN(C(=O)C(N)=O)CC1) `ZINC001486527909.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001486527909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001486527909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001486527909 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@H]1C1CCN(C(=O)C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 8, 1, 11, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 11, 23, 34, 34, 34, 34, 39, 39, 50, 50, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 34, 34, 34, 34, 34, 50, 50, 34, 34, 34, 34] 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]) total number of confs: 153 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001486527909 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001486527909/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001486527909 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 587) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/587 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/587' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@H]1C1CCN(C(=O)C(N)=O)CC1) `ZINC001486527909.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001486527909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001486527909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001486527909 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@H]1C1CCN(C(=O)C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 8, 1, 11, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 10, 20, 29, 29, 29, 29, 35, 35, 50, 50, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 29, 29, 29, 29, 29, 50, 50, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 160 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001486527909 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001486527909 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001486527909/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001486527909/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001486527909 Building ZINC001486527909 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001486527909' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001486527909 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001486527909 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001486527909/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001486527909 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 586) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/586: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@H]1C1CCN(C(=O)C(N)=O)CC1) `ZINC001486527909.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001486527909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001486527909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001486527909 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@H]1C1CCN(C(=O)C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 8, 1, 11, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 11, 23, 34, 34, 34, 34, 39, 39, 50, 50, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 34, 34, 34, 34, 34, 50, 50, 34, 34, 34, 34] 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]) total number of confs: 153 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001486527909 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001486527909/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001486527909 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 587) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/587: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@H]1C1CCN(C(=O)C(N)=O)CC1) `ZINC001486527909.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001486527909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001486527909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001486527909 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCO[C@H]1C1CCN(C(=O)C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 8, 1, 11, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 10, 20, 29, 29, 29, 29, 35, 35, 50, 50, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 29, 29, 29, 29, 29, 50, 50, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 160 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001486527909 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001486527909 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001486527909/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001486527909/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001486527909 Building ZINC001488428135 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428135' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428135 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001488428135 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428135/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428135 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/588 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1) `ZINC001488428135.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001488428135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001488428135 none CN(C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 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, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 16, 9, 6, 9, 9, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 28, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 16, 16, 27, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 45, 43, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 227 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428135 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428135/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428135 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 589) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/589 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/589' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1) `ZINC001488428135.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001488428135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428135/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001488428135 none CN(C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 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, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 21, 11, 7, 11, 11, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 30, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 21, 21, 33, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 45, 43, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 232 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428135 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001488428135 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428135/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428135/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428135 Building ZINC001488428135 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428135' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428135 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001488428135 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428135/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428135 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 588) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/588: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1) `ZINC001488428135.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001488428135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001488428135 none CN(C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 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, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 16, 9, 6, 9, 9, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 28, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 16, 16, 27, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 45, 43, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 227 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428135 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428135/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428135 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 589) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/589: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1) `ZINC001488428135.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001488428135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428135/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001488428135 none CN(C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 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, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 21, 11, 7, 11, 11, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 30, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 21, 21, 33, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 45, 43, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 232 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428135 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001488428135 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428135/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428135/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428135 Building ZINC001488428137 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428137' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428137 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001488428137 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428137/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428137 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/590 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1) `ZINC001488428137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001488428137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001488428137 none CN(C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 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, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 19, 10, 7, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 29, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 19, 19, 30, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 45, 43, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 225 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428137 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428137/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428137 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 591) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/591 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/591' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1) `ZINC001488428137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001488428137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001488428137 none CN(C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 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, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 16, 9, 6, 9, 9, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 24, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 16, 16, 27, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 45, 43, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 222 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428137 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001488428137 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428137/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428137/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428137 Building ZINC001488428137 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428137' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428137 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001488428137 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428137/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428137 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 590) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/590: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1) `ZINC001488428137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001488428137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001488428137 none CN(C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 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, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 19, 10, 7, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 29, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 19, 19, 30, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 45, 43, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 225 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428137 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428137/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428137 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 591) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/591: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1) `ZINC001488428137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001488428137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001488428137 none CN(C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC[C@@H](C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 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, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 16, 9, 6, 9, 9, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 24, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 16, 16, 27, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [48, 45, 43, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 222 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428137 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001488428137 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428137/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428137/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488428137 Building ZINC001488902729 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488902729' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488902729 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001488902729 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488902729/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488902729 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/592 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@H]1CC[C@@H](C(N)=O)O1)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001488902729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001488902729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488902729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001488902729 none CCN(C(=O)[C@H]1CC[C@@H](C(N)=O)O1)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 30, 24, 30, 39, 39, 42, 42, 42, 42, 42, 42, 43, 43, 42, 11, 24, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 42, 42, 42, 42, 43, 43, 24, 24, 24, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 205 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488902729 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488902729/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488902729 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 593) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/593 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/593' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@H]1CC[C@@H](C(N)=O)O1)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001488902729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001488902729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488902729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001488902729 none CCN(C(=O)[C@H]1CC[C@@H](C(N)=O)O1)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 32, 24, 32, 41, 42, 44, 44, 44, 44, 44, 44, 44, 44, 44, 12, 24, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 44, 44, 44, 44, 44, 44, 24, 24, 24, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 208 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488902729 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001488902729 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488902729/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488902729/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488902729 Building ZINC001488902729 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488902729' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488902729 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001488902729 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488902729/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488902729 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 592) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/592: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@H]1CC[C@@H](C(N)=O)O1)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001488902729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001488902729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488902729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001488902729 none CCN(C(=O)[C@H]1CC[C@@H](C(N)=O)O1)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 30, 24, 30, 39, 39, 42, 42, 42, 42, 42, 42, 43, 43, 42, 11, 24, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 42, 42, 42, 42, 43, 43, 24, 24, 24, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 205 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488902729 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488902729/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488902729 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 593) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/593: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@H]1CC[C@@H](C(N)=O)O1)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001488902729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001488902729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488902729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001488902729 none CCN(C(=O)[C@H]1CC[C@@H](C(N)=O)O1)[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 32, 24, 32, 41, 42, 44, 44, 44, 44, 44, 44, 44, 44, 44, 12, 24, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 44, 44, 44, 44, 44, 44, 24, 24, 24, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 208 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488902729 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001488902729 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488902729/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488902729/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001488902729 Building ZINC001489217758 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489217758' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489217758 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489217758 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489217758/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489217758 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/594 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)C3(NC(N)=O)CC3)C[C@H]21) `ZINC001489217758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489217758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489217758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489217758 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)C3(NC(N)=O)CC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8, 8, 8, 24, 24, 46, 50, 50, 50, 46, 46, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 50, 50, 50, 46, 46, 46, 46, 8, 8] 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]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489217758 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489217758/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489217758 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 595) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/595 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/595' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)C3(NC(N)=O)CC3)C[C@H]21) `ZINC001489217758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489217758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489217758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489217758 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)C3(NC(N)=O)CC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 9, 9, 9, 9, 9, 9, 9, 24, 24, 48, 50, 50, 50, 48, 48, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 50, 50, 50, 48, 48, 48, 48, 9, 9] 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]) total number of confs: 155 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489217758 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489217758 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489217758/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489217758/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489217758 Building ZINC001489217758 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489217758' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489217758 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489217758 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489217758/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489217758 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 594) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/594: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)C3(NC(N)=O)CC3)C[C@H]21) `ZINC001489217758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489217758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489217758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489217758 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)C3(NC(N)=O)CC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8, 8, 8, 24, 24, 46, 50, 50, 50, 46, 46, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 50, 50, 50, 46, 46, 46, 46, 8, 8] 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]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489217758 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489217758/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489217758 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 595) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/595: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)C3(NC(N)=O)CC3)C[C@H]21) `ZINC001489217758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489217758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489217758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489217758 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(C(=O)C3(NC(N)=O)CC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 9, 9, 9, 9, 9, 9, 9, 24, 24, 48, 50, 50, 50, 48, 48, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 50, 50, 50, 48, 48, 48, 48, 9, 9] 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]) total number of confs: 155 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489217758 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489217758 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489217758/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489217758/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489217758 Building ZINC001489224686 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489224686' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489224686 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489224686 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489224686/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489224686 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/596 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/596' -> `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]2CCN(C(=O)C3(NC(N)=O)CC3)[C@@H]2C1) `ZINC001489224686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489224686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489224686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489224686 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CCN(C(=O)C3(NC(N)=O)CC3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 10, 13, 13, 13, 13, 13, 13, 13, 30, 30, 47, 50, 50, 50, 47, 47, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 50, 50, 50, 47, 47, 47, 47, 13, 13] 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]) total number of confs: 151 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489224686 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489224686/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489224686 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 597) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/597 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/597' -> `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]2CCN(C(=O)C3(NC(N)=O)CC3)[C@@H]2C1) `ZINC001489224686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489224686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489224686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489224686 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CCN(C(=O)C3(NC(N)=O)CC3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 9, 13, 13, 13, 13, 13, 13, 13, 33, 33, 48, 50, 50, 50, 48, 48, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 50, 50, 50, 48, 48, 48, 48, 13, 13] 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]) total number of confs: 148 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489224686 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489224686 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489224686/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489224686/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489224686 Building ZINC001489224686 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489224686' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489224686 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489224686 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489224686/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489224686 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 596) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/596: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CCN(C(=O)C3(NC(N)=O)CC3)[C@@H]2C1) `ZINC001489224686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489224686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489224686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489224686 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2CCN(C(=O)C3(NC(N)=O)CC3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 10, 13, 13, 13, 13, 13, 13, 13, 30, 30, 47, 50, 50, 50, 47, 47, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 50, 50, 50, 47, 47, 47, 47, 13, 13] 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]) total number of confs: 151 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489224686 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489224686/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489224686 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 597) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/597: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CCN(C(=O)C3(NC(N)=O)CC3)[C@@H]2C1) `ZINC001489224686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489224686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489224686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489224686 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H]2CCN(C(=O)C3(NC(N)=O)CC3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 8, 1, 8, 11, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 9, 13, 13, 13, 13, 13, 13, 13, 33, 33, 48, 50, 50, 50, 48, 48, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 50, 50, 50, 48, 48, 48, 48, 13, 13] 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]) total number of confs: 148 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489224686 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489224686 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489224686/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489224686/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489224686 Building ZINC001489313690 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489313690' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489313690 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489313690 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489313690/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489313690 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/598 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3[nH]ncc3c2)C[C@H]1O) `ZINC001489313690.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489313690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489313690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001489313690 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3[nH]ncc3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489313690 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489313690/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489313690 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 599) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/599 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/599' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3[nH]ncc3c2)C[C@H]1O) `ZINC001489313690.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489313690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489313690/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001489313690 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3[nH]ncc3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489313690 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489313690 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489313690/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489313690/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489313690 Building ZINC001489313690 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489313690' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489313690 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489313690 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489313690/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489313690 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 598) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/598: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3[nH]ncc3c2)C[C@H]1O) `ZINC001489313690.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489313690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489313690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001489313690 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3[nH]ncc3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489313690 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489313690/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489313690 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 599) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/599: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3[nH]ncc3c2)C[C@H]1O) `ZINC001489313690.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489313690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489313690/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001489313690 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3[nH]ncc3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489313690 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489313690 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489313690/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489313690/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489313690 Building ZINC001489314107 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314107' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314107 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489314107 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314107/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314107 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/600 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001489314107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489314107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001489314107 none Cc1cc(OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 32, 12, 6, 12, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 32, 32, 6, 6, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46, 47]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314107 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314107/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314107 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 601) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/601 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/601' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001489314107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489314107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001489314107 none Cc1cc(OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 33, 11, 7, 11, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 33, 33, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314107 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489314107 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314107/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314107/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314107 Building ZINC001489314107 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314107' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314107 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489314107 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314107/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314107 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 600) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/600: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001489314107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489314107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001489314107 none Cc1cc(OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 32, 12, 6, 12, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 32, 32, 6, 6, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46, 47]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314107 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314107/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314107 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 601) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/601: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001489314107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489314107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001489314107 none Cc1cc(OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 33, 11, 7, 11, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 33, 33, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314107 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489314107 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314107/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314107/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314107 Building ZINC001489314187 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314187' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314187 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489314187 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314187/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314187 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/602 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCS(C)(=O)=O)C[C@H]1O) `ZINC001489314187.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489314187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001489314187 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCS(C)(=O)=O)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 14, 5, 11, 11, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 13, 13, 36, 34, 37, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 36, 36, 37, 37, 37, 37, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 252 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314187 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314187/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314187 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 603) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/603 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/603' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCS(C)(=O)=O)C[C@H]1O) `ZINC001489314187.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489314187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314187/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001489314187 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCS(C)(=O)=O)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 14, 5, 11, 11, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 13, 13, 32, 31, 37, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 32, 32, 37, 37, 37, 37, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314187 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489314187 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314187/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314187/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314187 Building ZINC001489314187 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314187' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314187 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489314187 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314187/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314187 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 602) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/602: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCS(C)(=O)=O)C[C@H]1O) `ZINC001489314187.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489314187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001489314187 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCS(C)(=O)=O)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 14, 5, 11, 11, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 13, 13, 36, 34, 37, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 36, 36, 37, 37, 37, 37, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 252 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314187 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314187/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314187 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 603) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/603: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCS(C)(=O)=O)C[C@H]1O) `ZINC001489314187.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489314187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314187/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001489314187 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCS(C)(=O)=O)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 14, 5, 11, 11, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 13, 13, 32, 31, 37, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 32, 32, 37, 37, 37, 37, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314187 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489314187 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314187/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314187/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314187 Building ZINC001489314971 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314971' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314971 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489314971 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314971/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314971 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/604 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCC(=O)NC2)C[C@H]1O) `ZINC001489314971.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489314971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489314971 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCC(=O)NC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 12, 12, 45, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 28, 28, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 168 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314971 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314971/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314971 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 605) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/605 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/605' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCC(=O)NC2)C[C@H]1O) `ZINC001489314971.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489314971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489314971 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCC(=O)NC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 12, 12, 42, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 26, 26, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314971 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489314971 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314971/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314971/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314971 Building ZINC001489314971 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314971' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314971 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489314971 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314971/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314971 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 604) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/604: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCC(=O)NC2)C[C@H]1O) `ZINC001489314971.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489314971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489314971 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCC(=O)NC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 12, 12, 45, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 28, 28, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 168 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314971 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314971/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314971 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 605) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/605: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCC(=O)NC2)C[C@H]1O) `ZINC001489314971.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489314971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489314971 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCC(=O)NC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 12, 12, 42, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 26, 26, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314971 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489314971 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314971/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314971/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314971 Building ZINC001489314973 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314973' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314973 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489314973 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314973/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314973 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/606 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCC(=O)NC2)C[C@H]1O) `ZINC001489314973.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489314973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489314973 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCC(=O)NC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 12, 12, 42, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 32, 32, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314973 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314973/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314973 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 607) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/607 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/607' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCC(=O)NC2)C[C@H]1O) `ZINC001489314973.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489314973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314973/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489314973 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCC(=O)NC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 10, 10, 40, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 30, 30, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314973 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489314973 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314973/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314973/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314973 Building ZINC001489314973 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314973' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314973 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489314973 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314973/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314973 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 606) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/606: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCC(=O)NC2)C[C@H]1O) `ZINC001489314973.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489314973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489314973 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCC(=O)NC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 12, 12, 42, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 32, 32, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314973 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314973/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314973 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 607) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/607: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCC(=O)NC2)C[C@H]1O) `ZINC001489314973.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489314973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314973/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489314973 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCC(=O)NC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 10, 10, 40, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 30, 30, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314973 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489314973 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314973/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314973/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489314973 Building ZINC001489315177 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315177' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315177 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489315177 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315177/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315177 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/608 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1Cl) `ZINC001489315177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489315177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001489315177 none Cn1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 16, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 25, 10, 25, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315177 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315177/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315177 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 609) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/609 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/609' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1Cl) `ZINC001489315177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489315177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001489315177 none Cn1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 16, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 25, 10, 25, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315177 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489315177 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315177/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315177/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315177 Building ZINC001489315177 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315177' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315177 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489315177 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315177/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315177 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 608) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/608: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1Cl) `ZINC001489315177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489315177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001489315177 none Cn1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 16, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 25, 10, 25, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315177 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315177/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315177 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 609) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/609: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1Cl) `ZINC001489315177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489315177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001489315177 none Cn1ncc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 16, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 25, 10, 25, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315177 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489315177 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315177/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315177/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315177 Building ZINC001489315584 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315584' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315584 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489315584 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315584/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315584 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/610 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1=O) `ZINC001489315584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489315584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489315584 none CN1CC[C@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 49, 50, 18, 10, 18, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315584 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315584/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315584 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 611) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/611 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/611' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1=O) `ZINC001489315584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489315584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489315584 none CN1CC[C@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 47, 50, 19, 8, 19, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315584 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489315584 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315584/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315584/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315584 Building ZINC001489315584 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315584' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315584 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489315584 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315584/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315584 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 610) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/610: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1=O) `ZINC001489315584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489315584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489315584 none CN1CC[C@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 49, 50, 18, 10, 18, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315584 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315584/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315584 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 611) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/611: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1=O) `ZINC001489315584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489315584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489315584 none CN1CC[C@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 47, 50, 19, 8, 19, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315584 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489315584 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315584/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315584/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315584 Building ZINC001489315585 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315585' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315585 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489315585 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315585/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315585 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/612 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1=O) `ZINC001489315585.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489315585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489315585 none CN1CC[C@@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 48, 50, 22, 10, 22, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315585 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315585/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315585 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 613) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/613 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/613' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1=O) `ZINC001489315585.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489315585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489315585 none CN1CC[C@@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 48, 50, 18, 9, 18, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315585 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489315585 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315585/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315585/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315585 Building ZINC001489315585 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315585' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315585 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489315585 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315585/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315585 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 612) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/612: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1=O) `ZINC001489315585.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489315585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489315585 none CN1CC[C@@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 48, 50, 22, 10, 22, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315585 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315585/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315585 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 613) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/613: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1=O) `ZINC001489315585.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489315585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489315585 none CN1CC[C@@H](CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 48, 50, 18, 9, 18, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315585 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489315585 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315585/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315585/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315585 Building ZINC001489315604 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001489315604 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/614 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@H](C(N)=O)CC2)C[C@H]1O) `ZINC001489315604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489315604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489315604 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@H](C(N)=O)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 11, 18, 31, 31, 31, 31, 31, 31, 50, 50, 31, 31, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 31, 31, 31, 31, 50, 50, 31, 31, 31, 31, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 179 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 615) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/615 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/615' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@H](C(N)=O)CC2)C[C@H]1O) `ZINC001489315604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489315604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489315604 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@H](C(N)=O)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 11, 18, 29, 29, 29, 29, 29, 29, 50, 50, 29, 29, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 29, 29, 29, 29, 50, 50, 29, 29, 29, 29, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 616) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/616 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/616' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)CC2)C[C@H]1O) `ZINC001489315604.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001489315604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489315604 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 11, 18, 31, 31, 31, 31, 31, 31, 50, 50, 31, 31, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 31, 31, 31, 31, 50, 50, 31, 31, 31, 31, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 179 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 617) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/617 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/617' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)CC2)C[C@H]1O) `ZINC001489315604.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001489315604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489315604 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 11, 18, 30, 30, 30, 30, 30, 30, 50, 50, 30, 30, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 30, 30, 30, 30, 50, 50, 30, 30, 30, 30, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489315604 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 Building ZINC001489315604 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001489315604 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 614) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/614: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@H](C(N)=O)CC2)C[C@H]1O) `ZINC001489315604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489315604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489315604 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@H](C(N)=O)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 11, 18, 31, 31, 31, 31, 31, 31, 50, 50, 31, 31, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 31, 31, 31, 31, 50, 50, 31, 31, 31, 31, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 179 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 615) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/615: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@H](C(N)=O)CC2)C[C@H]1O) `ZINC001489315604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489315604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489315604 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@H](C(N)=O)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 11, 18, 29, 29, 29, 29, 29, 29, 50, 50, 29, 29, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 29, 29, 29, 29, 50, 50, 29, 29, 29, 29, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 616) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/616: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)CC2)C[C@H]1O) `ZINC001489315604.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001489315604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489315604 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 11, 18, 31, 31, 31, 31, 31, 31, 50, 50, 31, 31, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 31, 31, 31, 31, 50, 50, 31, 31, 31, 31, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 179 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 617) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/617: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)CC2)C[C@H]1O) `ZINC001489315604.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001489315604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489315604 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 11, 18, 30, 30, 30, 30, 30, 30, 50, 50, 30, 30, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 30, 30, 30, 30, 50, 50, 30, 30, 30, 30, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489315604 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 Building ZINC001489315604 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001489315604 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 614) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/614: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@H](C(N)=O)CC2)C[C@H]1O) `ZINC001489315604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489315604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489315604 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@H](C(N)=O)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 11, 18, 31, 31, 31, 31, 31, 31, 50, 50, 31, 31, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 31, 31, 31, 31, 50, 50, 31, 31, 31, 31, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 179 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 615) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/615: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@H](C(N)=O)CC2)C[C@H]1O) `ZINC001489315604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489315604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489315604 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@H](C(N)=O)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 11, 18, 29, 29, 29, 29, 29, 29, 50, 50, 29, 29, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 29, 29, 29, 29, 50, 50, 29, 29, 29, 29, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 616) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/616: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)CC2)C[C@H]1O) `ZINC001489315604.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001489315604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489315604 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 11, 18, 31, 31, 31, 31, 31, 31, 50, 50, 31, 31, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 31, 31, 31, 31, 50, 50, 31, 31, 31, 31, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 179 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 617) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/617: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)CC2)C[C@H]1O) `ZINC001489315604.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001489315604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489315604 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 11, 18, 30, 30, 30, 30, 30, 30, 50, 50, 30, 30, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 30, 30, 30, 30, 50, 50, 30, 30, 30, 30, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489315604 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 Building ZINC001489315604 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001489315604 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 614) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/614: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@H](C(N)=O)CC2)C[C@H]1O) `ZINC001489315604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489315604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489315604 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@H](C(N)=O)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 11, 18, 31, 31, 31, 31, 31, 31, 50, 50, 31, 31, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 31, 31, 31, 31, 50, 50, 31, 31, 31, 31, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 179 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 615) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/615: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@H](C(N)=O)CC2)C[C@H]1O) `ZINC001489315604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489315604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489315604 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@H](C(N)=O)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 11, 18, 29, 29, 29, 29, 29, 29, 50, 50, 29, 29, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 29, 29, 29, 29, 50, 50, 29, 29, 29, 29, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 616) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/616: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)CC2)C[C@H]1O) `ZINC001489315604.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001489315604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489315604 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 11, 18, 31, 31, 31, 31, 31, 31, 50, 50, 31, 31, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 31, 31, 31, 31, 50, 50, 31, 31, 31, 31, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 179 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 617) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/617: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)CC2)C[C@H]1O) `ZINC001489315604.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001489315604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489315604 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)CC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 11, 18, 30, 30, 30, 30, 30, 30, 50, 50, 30, 30, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 30, 30, 30, 30, 50, 50, 30, 30, 30, 30, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489315604 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315604 Building ZINC001489315750 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315750' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315750 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489315750 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315750/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315750 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/618 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnc3[nH]cnc32)C[C@H]1O) `ZINC001489315750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489315750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001489315750 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnc3[nH]cnc32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'N.2', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 6, 1, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 50, 50, 50, 15, 15, 45] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315750 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315750/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315750 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 619) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/619 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/619' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnc3[nH]cnc32)C[C@H]1O) `ZINC001489315750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489315750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001489315750 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnc3[nH]cnc32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'N.2', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 6, 1, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315750 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489315750 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315750/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315750/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315750 Building ZINC001489315750 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315750' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315750 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489315750 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315750/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315750 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 618) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/618: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnc3[nH]cnc32)C[C@H]1O) `ZINC001489315750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489315750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001489315750 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnc3[nH]cnc32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'N.2', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 6, 1, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 50, 50, 50, 15, 15, 45] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315750 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315750/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315750 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 619) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/619: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnc3[nH]cnc32)C[C@H]1O) `ZINC001489315750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489315750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001489315750 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnc3[nH]cnc32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'N.2', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 6, 1, 8, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315750 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489315750 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315750/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315750/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315750 Building ZINC001489315766 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315766' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315766 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489315766 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315766/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315766 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/620 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3cncn3C2)C[C@H]1O) `ZINC001489315766.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489315766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489315766 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3cncn3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 23, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 171 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315766 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315766/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315766 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 621) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/621 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/621' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3cncn3C2)C[C@H]1O) `ZINC001489315766.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489315766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315766/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489315766 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3cncn3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 24, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 164 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315766 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489315766 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315766/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315766/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315766 Building ZINC001489315766 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315766' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315766 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489315766 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315766/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315766 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 620) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/620: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3cncn3C2)C[C@H]1O) `ZINC001489315766.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489315766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489315766 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3cncn3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 23, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 171 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315766 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315766/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315766 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 621) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/621: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3cncn3C2)C[C@H]1O) `ZINC001489315766.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489315766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315766/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489315766 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3cncn3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 24, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 164 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315766 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489315766 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315766/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315766/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315766 Building ZINC001489315769 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315769' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315769 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489315769 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315769/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315769 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/622 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3cncn3C2)C[C@H]1O) `ZINC001489315769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489315769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489315769 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3cncn3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 26, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 164 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315769 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315769/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315769 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 623) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/623 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/623' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3cncn3C2)C[C@H]1O) `ZINC001489315769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489315769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489315769 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3cncn3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 24, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 165 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315769 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489315769 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315769/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315769/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315769 Building ZINC001489315769 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315769' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315769 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489315769 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315769/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315769 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 622) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/622: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3cncn3C2)C[C@H]1O) `ZINC001489315769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489315769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489315769 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3cncn3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 26, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 164 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315769 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315769/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315769 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 623) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/623: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3cncn3C2)C[C@H]1O) `ZINC001489315769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489315769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489315769 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3cncn3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 24, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 165 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315769 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489315769 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315769/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315769/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489315769 Building ZINC001489316063 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316063' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316063 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489316063 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316063/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316063 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/624 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1cnc[nH]1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001489316063.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489316063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489316063 none C[C@@H](Cc1cnc[nH]1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [37, 23, 37, 37, 43, 50, 50, 50, 50, 50, 10, 23, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 37, 37, 37, 43, 43, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 225 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316063 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316063/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316063 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 625) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/625 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/625' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1cnc[nH]1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001489316063.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489316063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316063/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489316063 none C[C@@H](Cc1cnc[nH]1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 24, 38, 38, 45, 50, 50, 50, 50, 50, 9, 24, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 38, 38, 38, 45, 45, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 217 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316063 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489316063 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316063/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316063/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316063 Building ZINC001489316063 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316063' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316063 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489316063 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316063/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316063 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 624) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/624: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1cnc[nH]1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001489316063.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489316063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489316063 none C[C@@H](Cc1cnc[nH]1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [37, 23, 37, 37, 43, 50, 50, 50, 50, 50, 10, 23, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 37, 37, 37, 43, 43, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 225 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316063 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316063/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316063 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 625) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/625: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1cnc[nH]1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001489316063.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489316063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316063/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489316063 none C[C@@H](Cc1cnc[nH]1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 24, 38, 38, 45, 50, 50, 50, 50, 50, 9, 24, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 38, 38, 38, 45, 45, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 217 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316063 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489316063 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316063/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316063/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316063 Building ZINC001489316065 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316065' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316065 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489316065 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316065/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316065 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/626 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cnc[nH]1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001489316065.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489316065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489316065 none C[C@H](Cc1cnc[nH]1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [35, 20, 35, 35, 44, 50, 50, 50, 50, 50, 8, 20, 8, 8, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 35, 35, 35, 44, 44, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/323031/xbw-8058115.49/working/building/ZINC001489316065 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316065/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316065 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 627) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/627 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/627' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cnc[nH]1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001489316065.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489316065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316065/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489316065 none C[C@H](Cc1cnc[nH]1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 19, 32, 32, 44, 50, 50, 50, 50, 50, 10, 19, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 32, 32, 32, 44, 44, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 220 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316065 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489316065 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316065/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316065/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316065 Building ZINC001489316065 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316065' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316065 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489316065 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316065/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316065 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 626) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/626: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cnc[nH]1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001489316065.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489316065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489316065 none C[C@H](Cc1cnc[nH]1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [35, 20, 35, 35, 44, 50, 50, 50, 50, 50, 8, 20, 8, 8, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 35, 35, 35, 44, 44, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/323031/xbw-8058115.49/working/building/ZINC001489316065 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316065/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316065 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 627) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/627: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cnc[nH]1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001489316065.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489316065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316065/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489316065 none C[C@H](Cc1cnc[nH]1)C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 19, 32, 32, 44, 50, 50, 50, 50, 50, 10, 19, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 32, 32, 32, 44, 44, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 220 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316065 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489316065 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316065/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316065/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316065 Building ZINC001489316462 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316462' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316462 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489316462 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316462/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316462 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/628 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1) `ZINC001489316462.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489316462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489316462 none Cc1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 34, 10, 7, 10, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 34, 34, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316462 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316462/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316462 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 629) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/629 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/629' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1) `ZINC001489316462.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489316462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316462/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489316462 none Cc1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 39, 12, 7, 12, 7, 7, 7, 7, 7, 4, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 39, 39, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 183 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316462 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489316462 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316462/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316462/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316462 Building ZINC001489316462 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316462' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316462 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489316462 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316462/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316462 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 628) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/628: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1) `ZINC001489316462.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489316462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489316462 none Cc1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 34, 10, 7, 10, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 34, 34, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316462 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316462/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316462 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 629) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/629: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1) `ZINC001489316462.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489316462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316462/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489316462 none Cc1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 39, 12, 7, 12, 7, 7, 7, 7, 7, 4, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 39, 39, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 183 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316462 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489316462 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316462/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316462/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316462 Building ZINC001489316465 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316465' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316465 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489316465 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316465/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316465 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/630 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001489316465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489316465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489316465 none CCC(=O)N1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 39, 45, 39, 39, 39, 13, 39, 7, 13, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 39, 50, 50, 50, 50, 50, 39, 39, 39, 39, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 39, 39] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316465 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316465/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316465 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 631) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/631 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/631' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001489316465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489316465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489316465 none CCC(=O)N1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 46, 39, 46, 39, 39, 39, 14, 39, 9, 14, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 39, 50, 50, 50, 50, 50, 39, 39, 39, 39, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 39, 39] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 188 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316465 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489316465 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316465/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316465/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316465 Building ZINC001489316465 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316465' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316465 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489316465 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316465/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316465 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 630) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/630: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001489316465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489316465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489316465 none CCC(=O)N1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 39, 45, 39, 39, 39, 13, 39, 7, 13, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 39, 50, 50, 50, 50, 50, 39, 39, 39, 39, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 39, 39] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316465 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316465/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316465 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 631) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/631: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001489316465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489316465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489316465 none CCC(=O)N1CC[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 46, 39, 46, 39, 39, 39, 14, 39, 9, 14, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 39, 50, 50, 50, 50, 50, 39, 39, 39, 39, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 39, 39] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 188 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316465 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489316465 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316465/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316465/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316465 Building ZINC001489316469 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316469' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316469 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489316469 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316469/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316469 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/632 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001489316469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489316469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489316469 none CCC(=O)N1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 39, 45, 39, 39, 39, 14, 39, 9, 14, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 39, 50, 50, 50, 50, 50, 39, 39, 39, 39, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 39, 39] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 188 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316469 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316469/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316469 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 633) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/633 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/633' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001489316469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489316469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489316469 none CCC(=O)N1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 44, 40, 44, 40, 40, 40, 13, 40, 7, 13, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 40, 50, 50, 50, 50, 50, 40, 40, 40, 40, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 40, 40] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 188 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316469 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489316469 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316469/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316469/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316469 Building ZINC001489316469 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316469' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316469 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489316469 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316469/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316469 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 632) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/632: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001489316469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489316469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489316469 none CCC(=O)N1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 39, 45, 39, 39, 39, 14, 39, 9, 14, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 39, 50, 50, 50, 50, 50, 39, 39, 39, 39, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 39, 39] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 188 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316469 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316469/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316469 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 633) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/633: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001489316469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489316469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489316469 none CCC(=O)N1CC[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 44, 40, 44, 40, 40, 40, 13, 40, 7, 13, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 40, 50, 50, 50, 50, 50, 40, 40, 40, 40, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 40, 40] 150 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 188 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316469 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489316469 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316469/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316469/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316469 Building ZINC001489316479 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316479' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316479 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489316479 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316479/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316479 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/634 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001489316479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489316479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001489316479 none CCCNC(=O)CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 35, 35, 30, 35, 22, 18, 10, 7, 10, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 35, 28, 29, 24, 24, 18, 18, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 264 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316479 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316479/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316479 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 635) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/635 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/635' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001489316479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489316479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001489316479 none CCCNC(=O)CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 33, 28, 33, 22, 20, 12, 7, 12, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 33, 26, 28, 24, 24, 20, 20, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 273 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316479 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489316479 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316479/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316479/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316479 Building ZINC001489316479 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316479' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316479 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489316479 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316479/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316479 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 634) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/634: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001489316479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489316479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001489316479 none CCCNC(=O)CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 35, 35, 30, 35, 22, 18, 10, 7, 10, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 35, 28, 29, 24, 24, 18, 18, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 264 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316479 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316479/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316479 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 635) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/635: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001489316479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489316479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001489316479 none CCCNC(=O)CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 33, 28, 33, 22, 20, 12, 7, 12, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 33, 26, 28, 24, 24, 20, 20, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 273 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316479 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489316479 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316479/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316479/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316479 Building ZINC001489316563 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316563' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316563 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489316563 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316563/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316563 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/636 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3n2CCOC3)C[C@H]1O) `ZINC001489316563.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489316563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001489316563 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3n2CCOC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 20, 20, 20, 20, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 20, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20, 60] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316563 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316563/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316563 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 637) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/637 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/637' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3n2CCOC3)C[C@H]1O) `ZINC001489316563.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489316563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316563/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001489316563 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3n2CCOC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 18, 18, 18, 18, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 50, 50, 50, 50, 50, 50, 50, 18, 18, 54] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316563 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489316563 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316563/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316563/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316563 Building ZINC001489316563 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316563' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316563 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489316563 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316563/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316563 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 636) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/636: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3n2CCOC3)C[C@H]1O) `ZINC001489316563.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489316563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001489316563 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3n2CCOC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 20, 20, 20, 20, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 20, 20, 50, 50, 50, 50, 50, 50, 50, 20, 20, 60] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316563 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316563/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316563 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 637) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/637: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3n2CCOC3)C[C@H]1O) `ZINC001489316563.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489316563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316563/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001489316563 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3n2CCOC3)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 18, 18, 18, 18, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 50, 50, 50, 50, 50, 50, 50, 18, 18, 54] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316563 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489316563 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316563/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316563/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316563 Building ZINC001489316683 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316683' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316683 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489316683 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316683/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316683 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/638 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3nccnc3c2)C[C@H]1O) `ZINC001489316683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489316683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489316683 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3nccnc3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 8, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 50, 50, 50, 50, 14, 14, 42] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316683 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316683/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316683 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 639) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/639 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/639' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3nccnc3c2)C[C@H]1O) `ZINC001489316683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489316683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489316683 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3nccnc3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 8, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316683 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489316683 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316683/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316683/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316683 Building ZINC001489316683 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316683' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316683 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489316683 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316683/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316683 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 638) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/638: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3nccnc3c2)C[C@H]1O) `ZINC001489316683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489316683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489316683 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3nccnc3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 8, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 50, 50, 50, 50, 14, 14, 42] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316683 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316683/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316683 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 639) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/639: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3nccnc3c2)C[C@H]1O) `ZINC001489316683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489316683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489316683 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3nccnc3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 8, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316683 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489316683 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316683/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316683/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316683 Building ZINC001489316968 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316968' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316968 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489316968 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316968/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316968 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/640 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn3nnnc3c2)C[C@H]1O) `ZINC001489316968.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489316968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001489316968 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn3nnnc3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 8, 8, 8, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316968 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316968/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316968 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 641) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/641 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/641' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn3nnnc3c2)C[C@H]1O) `ZINC001489316968.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489316968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316968/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001489316968 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn3nnnc3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 8, 8, 8, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316968 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489316968 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316968/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316968/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316968 Building ZINC001489316968 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316968' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316968 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489316968 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316968/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316968 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 640) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/640: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn3nnnc3c2)C[C@H]1O) `ZINC001489316968.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489316968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001489316968 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn3nnnc3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 8, 8, 8, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316968 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316968/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316968 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 641) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/641: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn3nnnc3c2)C[C@H]1O) `ZINC001489316968.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489316968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316968/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001489316968 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccn3nnnc3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 8, 8, 8, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316968 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489316968 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316968/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316968/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316968 Building ZINC001489316988 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316988' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316988 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489316988 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316988/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316988 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/642 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cn(CC3CC3)nn2)C[C@H]1O) `ZINC001489316988.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489316988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489316988 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cn(CC3CC3)nn2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 13, 13, 28, 28, 28, 50, 50, 50, 28, 28, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 28, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316988 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316988/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316988 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 643) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/643 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/643' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cn(CC3CC3)nn2)C[C@H]1O) `ZINC001489316988.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489316988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316988/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489316988 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cn(CC3CC3)nn2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 10, 10, 24, 24, 24, 50, 50, 50, 24, 24, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 24, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316988 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489316988 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316988/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316988/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316988 Building ZINC001489316988 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316988' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316988 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489316988 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316988/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316988 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 642) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/642: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cn(CC3CC3)nn2)C[C@H]1O) `ZINC001489316988.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489316988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489316988 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cn(CC3CC3)nn2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 13, 13, 28, 28, 28, 50, 50, 50, 28, 28, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 28, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316988 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316988/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316988 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 643) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/643: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cn(CC3CC3)nn2)C[C@H]1O) `ZINC001489316988.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489316988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316988/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489316988 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cn(CC3CC3)nn2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 10, 10, 24, 24, 24, 50, 50, 50, 24, 24, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 24, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316988 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489316988 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316988/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316988/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489316988 Building ZINC001489317479 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317479' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317479 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489317479 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317479/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317479 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/644 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1coc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cc1=O) `ZINC001489317479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489317479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001489317479 none COc1coc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 19, 11, 19, 11, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317479 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317479/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317479 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 645) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/645 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/645' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1coc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cc1=O) `ZINC001489317479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489317479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001489317479 none COc1coc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 16, 7, 16, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317479 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489317479 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317479/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317479/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317479 Building ZINC001489317479 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317479' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317479 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489317479 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317479/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317479 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 644) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/644: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1coc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cc1=O) `ZINC001489317479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489317479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001489317479 none COc1coc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 19, 11, 19, 11, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317479 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317479/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317479 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 645) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/645: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1coc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cc1=O) `ZINC001489317479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489317479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001489317479 none COc1coc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 16, 7, 16, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317479 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489317479 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317479/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317479/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317479 Building ZINC001489317554 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317554' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317554 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489317554 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317554/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317554 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/646 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001489317554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489317554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001489317554 none CCn1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 38, 38, 38, 31, 14, 8, 14, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 38, 38, 50, 50, 50, 50, 50, 38, 31, 31, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317554 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317554/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317554 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 647) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/647 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/647' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001489317554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489317554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001489317554 none CCn1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 35, 35, 35, 30, 14, 9, 14, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 35, 35, 50, 50, 50, 50, 50, 35, 30, 30, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317554 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489317554 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317554/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317554/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317554 Building ZINC001489317554 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317554' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317554 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489317554 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317554/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317554 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 646) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/646: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001489317554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489317554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001489317554 none CCn1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 38, 38, 38, 31, 14, 8, 14, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 38, 38, 50, 50, 50, 50, 50, 38, 31, 31, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317554 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317554/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317554 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 647) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/647: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001489317554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489317554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001489317554 none CCn1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 35, 35, 35, 30, 14, 9, 14, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 35, 35, 50, 50, 50, 50, 50, 35, 30, 30, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317554 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489317554 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317554/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317554/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317554 Building ZINC001489317595 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317595' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317595 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489317595 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317595/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317595 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/648 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cncc3nc[nH]c32)C[C@H]1O) `ZINC001489317595.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489317595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001489317595 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cncc3nc[nH]c32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 8, 6, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317595 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317595/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317595 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 649) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/649 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/649' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cncc3nc[nH]c32)C[C@H]1O) `ZINC001489317595.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489317595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001489317595 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cncc3nc[nH]c32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 8, 6, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317595 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489317595 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317595/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317595/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317595 Building ZINC001489317595 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317595' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317595 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489317595 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317595/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317595 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 648) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/648: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cncc3nc[nH]c32)C[C@H]1O) `ZINC001489317595.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489317595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001489317595 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cncc3nc[nH]c32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 8, 6, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317595 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317595/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317595 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 649) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/649: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cncc3nc[nH]c32)C[C@H]1O) `ZINC001489317595.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489317595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001489317595 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cncc3nc[nH]c32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 8, 6, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317595 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489317595 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317595/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317595/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317595 Building ZINC001489317962 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317962' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317962 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489317962 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317962/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317962 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/650 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1=O) `ZINC001489317962.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489317962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489317962 none CC[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 37, 24, 37, 14, 24, 14, 14, 14, 14, 14, 2, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 37, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 14, 14, 42, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317962 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317962/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317962 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 651) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/651 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/651' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1=O) `ZINC001489317962.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489317962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317962/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489317962 none CC[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 38, 23, 38, 14, 23, 14, 14, 14, 14, 14, 3, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 38, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 14, 14, 42, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317962 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489317962 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317962/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317962/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317962 Building ZINC001489317962 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317962' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317962 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489317962 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317962/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317962 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 650) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/650: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1=O) `ZINC001489317962.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489317962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489317962 none CC[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 37, 24, 37, 14, 24, 14, 14, 14, 14, 14, 2, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 37, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 14, 14, 42, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317962 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317962/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317962 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 651) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/651: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1=O) `ZINC001489317962.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489317962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317962/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489317962 none CC[C@@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 38, 23, 38, 14, 23, 14, 14, 14, 14, 14, 3, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 38, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 14, 14, 42, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317962 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489317962 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317962/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317962/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317962 Building ZINC001489317964 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317964' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317964 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489317964 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317964/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317964 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/652 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1=O) `ZINC001489317964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489317964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489317964 none CC[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 35, 25, 35, 11, 25, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 35, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317964 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317964/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317964 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 653) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/653 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/653' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1=O) `ZINC001489317964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489317964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489317964 none CC[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 38, 26, 38, 13, 26, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 38, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 13, 13, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317964 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489317964 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317964/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317964/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317964 Building ZINC001489317964 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317964' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317964 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489317964 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317964/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317964 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 652) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/652: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1=O) `ZINC001489317964.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489317964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489317964 none CC[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 35, 25, 35, 11, 25, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 35, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317964 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317964/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317964 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 653) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/653: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1=O) `ZINC001489317964.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489317964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489317964 none CC[C@H](C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 38, 26, 38, 13, 26, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 38, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 13, 13, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317964 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489317964 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317964/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317964/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489317964 Building ZINC001489318063 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318063' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318063 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489318063 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318063/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318063 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/654 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001489318063.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489318063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001489318063 none Cn1cc(OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 49, 41, 30, 10, 7, 10, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 30, 30, 7, 7, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46, 47, 48]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318063 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318063/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318063 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 655) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/655 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/655' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001489318063.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489318063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318063/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001489318063 none Cn1cc(OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 40, 25, 9, 6, 9, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 25, 25, 6, 6, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46, 47, 48]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318063 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489318063 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318063/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318063/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318063 Building ZINC001489318063 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318063' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318063 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489318063 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318063/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318063 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 654) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/654: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001489318063.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489318063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001489318063 none Cn1cc(OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 49, 41, 30, 10, 7, 10, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 30, 30, 7, 7, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46, 47, 48]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318063 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318063/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318063 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 655) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/655: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001489318063.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489318063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318063/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001489318063 none Cn1cc(OCC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 12, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 40, 25, 9, 6, 9, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 25, 25, 6, 6, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46, 47, 48]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318063 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489318063 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318063/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318063/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318063 Building ZINC001489318071 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318071' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318071 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489318071 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318071/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318071 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/656 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1) `ZINC001489318071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489318071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489318071 none CCc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 35, 35, 35, 19, 8, 19, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 35, 35, 35, 50, 50, 50, 50, 50, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 35, 35, 35] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318071 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318071/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318071 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 657) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/657 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/657' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1) `ZINC001489318071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489318071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489318071 none CCc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 33, 33, 33, 16, 7, 16, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 33, 33, 33, 50, 50, 50, 50, 50, 33, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318071 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489318071 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318071/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318071/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318071 Building ZINC001489318071 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318071' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318071 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489318071 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318071/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318071 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 656) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/656: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1) `ZINC001489318071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489318071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489318071 none CCc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 35, 35, 35, 19, 8, 19, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 35, 35, 35, 50, 50, 50, 50, 50, 35, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 35, 35, 35] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318071 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318071/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318071 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 657) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/657: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1) `ZINC001489318071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489318071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489318071 none CCc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 33, 33, 33, 16, 7, 16, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 33, 33, 33, 50, 50, 50, 50, 50, 33, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318071 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489318071 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318071/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318071/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318071 Building ZINC001489318511 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318511' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318511 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489318511 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318511/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318511 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/658 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001489318511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489318511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001489318511 none COCc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 28, 28, 28, 11, 6, 11, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 28, 28, 50, 50, 50, 50, 50, 28, 6, 6, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318511 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318511/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318511 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 659) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/659 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/659' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001489318511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489318511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001489318511 none COCc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 26, 26, 26, 11, 7, 11, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 26, 26, 50, 50, 50, 50, 50, 26, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318511 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489318511 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318511/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318511/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318511 Building ZINC001489318511 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318511' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318511 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489318511 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318511/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318511 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 658) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/658: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001489318511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489318511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001489318511 none COCc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 28, 28, 28, 11, 6, 11, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 28, 28, 50, 50, 50, 50, 50, 28, 6, 6, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318511 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318511/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318511 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 659) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/659: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001489318511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489318511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001489318511 none COCc1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 26, 26, 26, 11, 7, 11, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 26, 26, 50, 50, 50, 50, 50, 26, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318511 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489318511 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318511/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318511/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489318511 Building ZINC001489347800 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489347800' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489347800 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489347800 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489347800/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489347800 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/660 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)S(=O)(=O)CC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001489347800.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489347800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489347800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001489347800 none CC(C)S(=O)(=O)CC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 24, 24, 24, 10, 10, 10, 10, 4, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 30] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489347800 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489347800/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489347800 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 661) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/661 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/661' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)S(=O)(=O)CC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001489347800.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489347800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489347800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001489347800 none CC(C)S(=O)(=O)CC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 47, 50, 50, 18, 18, 18, 6, 6, 6, 6, 4, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 47, 47, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489347800 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489347800 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489347800/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489347800/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489347800 Building ZINC001489347800 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489347800' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489347800 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489347800 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489347800/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489347800 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 660) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/660: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)S(=O)(=O)CC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001489347800.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489347800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489347800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001489347800 none CC(C)S(=O)(=O)CC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 24, 24, 24, 10, 10, 10, 10, 4, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 30] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489347800 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489347800/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489347800 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 661) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/661: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)S(=O)(=O)CC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001489347800.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489347800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489347800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001489347800 none CC(C)S(=O)(=O)CC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 47, 50, 50, 18, 18, 18, 6, 6, 6, 6, 4, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 47, 47, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489347800 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489347800 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489347800/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489347800/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489347800 Building ZINC001489365470 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489365470' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489365470 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489365470 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489365470/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489365470 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/662 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCn2ccnc2)C1) `ZINC001489365470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489365470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489365470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489365470 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCn2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 21, 19, 29, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 4, 21, 21, 28, 28, 29, 28, 50, 50, 50, 1, 1] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 49, 50] set([48, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489365470 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489365470/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489365470 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 663) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/663 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/663' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCn2ccnc2)C1) `ZINC001489365470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489365470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489365470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489365470 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCn2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 19, 18, 29, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 19, 19, 25, 25, 27, 28, 50, 50, 50, 1, 1] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 49, 50] set([48, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489365470 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489365470 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489365470/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489365470/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489365470 Building ZINC001489365470 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489365470' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489365470 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489365470 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489365470/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489365470 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 662) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/662: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCn2ccnc2)C1) `ZINC001489365470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489365470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489365470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489365470 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCn2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 21, 19, 29, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 4, 21, 21, 28, 28, 29, 28, 50, 50, 50, 1, 1] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 49, 50] set([48, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489365470 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489365470/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489365470 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 663) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/663: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCn2ccnc2)C1) `ZINC001489365470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489365470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489365470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489365470 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCCn2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 19, 18, 29, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 19, 19, 25, 25, 27, 28, 50, 50, 50, 1, 1] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 49, 50] set([48, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489365470 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489365470 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489365470/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489365470/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489365470 Building ZINC001489376911 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489376911' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489376911 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489376911 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489376911/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489376911 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/664 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001489376911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489376911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489376911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001489376911 none CC(C)NC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 44, 50, 32, 25, 4, 4, 4, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 43, 44, 34, 34, 25, 25, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489376911 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489376911/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489376911 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 665) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/665 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/665' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001489376911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489376911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489376911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001489376911 none CC(C)NC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 36, 50, 25, 19, 4, 4, 4, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 25, 25, 19, 19, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489376911 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489376911 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489376911/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489376911/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489376911 Building ZINC001489376911 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489376911' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489376911 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489376911 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489376911/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489376911 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 664) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/664: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001489376911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489376911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489376911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001489376911 none CC(C)NC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 44, 50, 32, 25, 4, 4, 4, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 43, 44, 34, 34, 25, 25, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489376911 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489376911/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489376911 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 665) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/665: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O) `ZINC001489376911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489376911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489376911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001489376911 none CC(C)NC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 36, 50, 25, 19, 4, 4, 4, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 25, 25, 19, 19, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489376911 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489376911 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489376911/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489376911/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489376911 Building ZINC001489392424 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001489392424 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/666 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@](C)CC2)C1) `ZINC001489392424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489392424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489392424 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@](C)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 21, 44, 50, 50, 50, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 7, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 667) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/667 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/667' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@](C)CC2)C1) `ZINC001489392424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489392424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489392424 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@](C)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 20, 44, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 668) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/668 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/668' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)C1) `ZINC001489392424.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001489392424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489392424 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 22, 45, 50, 50, 50, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 8, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 669) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/669 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/669' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)C1) `ZINC001489392424.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001489392424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489392424 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 21, 44, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489392424 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 Building ZINC001489392424 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001489392424 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 666) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/666: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@](C)CC2)C1) `ZINC001489392424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489392424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489392424 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@](C)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 21, 44, 50, 50, 50, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 7, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 667) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/667: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@](C)CC2)C1) `ZINC001489392424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489392424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489392424 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@](C)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 20, 44, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 668) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/668: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)C1) `ZINC001489392424.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001489392424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489392424 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 22, 45, 50, 50, 50, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 8, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 669) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/669: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)C1) `ZINC001489392424.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001489392424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489392424 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 21, 44, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489392424 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 Building ZINC001489392424 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001489392424 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 666) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/666: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@](C)CC2)C1) `ZINC001489392424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489392424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489392424 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@](C)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 21, 44, 50, 50, 50, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 7, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 667) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/667: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@](C)CC2)C1) `ZINC001489392424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489392424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489392424 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@](C)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 20, 44, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 668) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/668: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)C1) `ZINC001489392424.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001489392424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489392424 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 22, 45, 50, 50, 50, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 8, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 669) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/669: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)C1) `ZINC001489392424.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001489392424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489392424 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 21, 44, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489392424 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 Building ZINC001489392424 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001489392424 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 666) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/666: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@](C)CC2)C1) `ZINC001489392424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489392424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489392424 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@](C)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 21, 44, 50, 50, 50, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 7, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 667) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/667: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@](C)CC2)C1) `ZINC001489392424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489392424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489392424 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@](C)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 20, 44, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 668) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/668: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)C1) `ZINC001489392424.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001489392424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489392424 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 22, 45, 50, 50, 50, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 8, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 669) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/669: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)C1) `ZINC001489392424.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001489392424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489392424 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CO[C@H]2CC[N@@](C)CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', '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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 7, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 21, 44, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489392424 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489392424 Building ZINC001489512412 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489512412' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489512412 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489512412 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489512412/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489512412 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/670 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)CCn2ccnn2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001489512412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489512412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489512412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001489512412 none CO[C@@H]1CN(C(=O)CCn2ccnn2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 13, 13, 13, 13, 13, 13, 20, 20, 34, 36, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 13, 13, 34, 34, 36, 36, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489512412 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489512412/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489512412 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 671) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/671 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/671' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)CCn2ccnn2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001489512412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489512412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489512412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001489512412 none CO[C@@H]1CN(C(=O)CCn2ccnn2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 10, 10, 10, 10, 10, 10, 18, 18, 34, 36, 50, 50, 50, 50, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 10, 10, 34, 34, 36, 36, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489512412 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489512412 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489512412/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489512412/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489512412 Building ZINC001489512412 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489512412' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489512412 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489512412 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489512412/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489512412 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 670) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/670: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)CCn2ccnn2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001489512412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489512412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489512412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001489512412 none CO[C@@H]1CN(C(=O)CCn2ccnn2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 13, 13, 13, 13, 13, 13, 20, 20, 34, 36, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 13, 13, 34, 34, 36, 36, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489512412 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489512412/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489512412 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 671) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/671: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)CCn2ccnn2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001489512412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489512412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489512412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001489512412 none CO[C@@H]1CN(C(=O)CCn2ccnn2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 10, 10, 10, 10, 10, 10, 18, 18, 34, 36, 50, 50, 50, 50, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 10, 10, 34, 34, 36, 36, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489512412 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489512412 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489512412/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489512412/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489512412 Building ZINC001489513719 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489513719' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489513719 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489513719 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489513719/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489513719 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/672 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)cnn1C) `ZINC001489513719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489513719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489513719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489513719 none COc1c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 24, 13, 24, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 19, 13, 48, 48, 48, 48, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 13, 13, 48, 48, 48, 48] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489513719 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489513719/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489513719 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 673) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/673 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/673' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)cnn1C) `ZINC001489513719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489513719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489513719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489513719 none COc1c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 9, 19, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 15, 9, 46, 46, 46, 46, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 9, 9, 46, 46, 46, 46] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489513719 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489513719 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489513719/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489513719/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489513719 Building ZINC001489513719 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489513719' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489513719 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489513719 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489513719/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489513719 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 672) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/672: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)cnn1C) `ZINC001489513719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489513719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489513719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489513719 none COc1c(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 24, 13, 24, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 19, 13, 48, 48, 48, 48, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 13, 13, 48, 48, 48, 48] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489513719 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489513719/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489513719 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 673) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/673: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)cnn1C) `ZINC001489513719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489513719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489513719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489513719 none COc1c(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 9, 19, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 15, 9, 46, 46, 46, 46, 50, 50, 50, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 9, 9, 46, 46, 46, 46] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489513719 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489513719 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489513719/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489513719/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489513719 Building ZINC001489515969 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489515969' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489515969 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489515969 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489515969/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489515969 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/674 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001489515969.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489515969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489515969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001489515969 none CNC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 33, 25, 6, 6, 6, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 6, 50, 50, 50, 50, 45, 44, 39, 39, 25, 25, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489515969 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489515969/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489515969 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 675) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/675 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/675' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001489515969.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489515969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489515969/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001489515969 none CNC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 50, 29, 29, 5, 5, 5, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 50, 50, 50, 50, 45, 45, 38, 38, 29, 29, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489515969 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489515969 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489515969/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489515969/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489515969 Building ZINC001489515969 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489515969' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489515969 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489515969 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489515969/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489515969 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 674) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/674: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001489515969.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489515969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489515969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001489515969 none CNC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 33, 25, 6, 6, 6, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 6, 50, 50, 50, 50, 45, 44, 39, 39, 25, 25, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489515969 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489515969/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489515969 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 675) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/675: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001489515969.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489515969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489515969/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001489515969 none CNC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 50, 29, 29, 5, 5, 5, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 50, 50, 50, 50, 45, 45, 38, 38, 29, 29, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489515969 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489515969 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489515969/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489515969/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489515969 Building ZINC001489532257 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489532257' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489532257 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489532257 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489532257/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489532257 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/676 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCN1CCOCC1) `ZINC001489532257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489532257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489532257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001489532257 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 9, 9, 9, 28, 29, 50, 50, 50, 50, 50, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 28, 28, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489532257 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489532257/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489532257 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 677) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/677 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/677' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCN1CCOCC1) `ZINC001489532257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489532257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489532257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001489532257 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 9, 9, 9, 35, 37, 50, 50, 50, 50, 50, 7, 7, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 35, 35, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489532257 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489532257 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489532257/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489532257/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489532257 Building ZINC001489532257 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489532257' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489532257 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489532257 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489532257/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489532257 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 676) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/676: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCN1CCOCC1) `ZINC001489532257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489532257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489532257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001489532257 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 9, 9, 9, 28, 29, 50, 50, 50, 50, 50, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 28, 28, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489532257 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489532257/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489532257 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 677) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/677: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCN1CCOCC1) `ZINC001489532257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489532257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489532257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001489532257 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 9, 9, 9, 35, 37, 50, 50, 50, 50, 50, 7, 7, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 35, 35, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489532257 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489532257 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489532257/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489532257/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489532257 Building ZINC001489548379 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548379' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548379 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489548379 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548379/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548379 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/678 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001489548379.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489548379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001489548379 none CC[C@@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 39, 10, 39, 39, 48, 48, 48, 10, 10, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 49, 49, 49, 49, 49, 48, 48, 48, 48, 10, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548379 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548379/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548379 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 679) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/679 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/679' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001489548379.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489548379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548379/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001489548379 none CC[C@@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 11, 37, 37, 48, 48, 48, 11, 11, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 6, 50, 50, 50, 50, 50, 48, 48, 48, 48, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 296 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548379 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489548379 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548379/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548379/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548379 Building ZINC001489548379 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548379' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548379 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489548379 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548379/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548379 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 678) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/678: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001489548379.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489548379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001489548379 none CC[C@@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 39, 10, 39, 39, 48, 48, 48, 10, 10, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 6, 49, 49, 49, 49, 49, 48, 48, 48, 48, 10, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 285 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548379 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548379/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548379 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 679) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/679: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001489548379.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489548379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548379/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001489548379 none CC[C@@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 11, 37, 37, 48, 48, 48, 11, 11, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 6, 50, 50, 50, 50, 50, 48, 48, 48, 48, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 6] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 296 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548379 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489548379 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548379/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548379/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548379 Building ZINC001489548380 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548380' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548380 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489548380 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548380/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548380 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/680 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001489548380.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489548380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001489548380 none CC[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 38, 10, 38, 38, 49, 49, 49, 10, 10, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 48, 48, 48, 48, 48, 49, 49, 49, 49, 10, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 276 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548380 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548380/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548380 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 681) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/681 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/681' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001489548380.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489548380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001489548380 none CC[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 39, 39, 46, 46, 46, 11, 11, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 50, 50, 50, 50, 50, 46, 46, 46, 46, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 306 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548380 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489548380 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548380/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548380/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548380 Building ZINC001489548380 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548380' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548380 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489548380 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548380/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548380 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 680) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/680: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001489548380.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489548380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001489548380 none CC[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 38, 10, 38, 38, 49, 49, 49, 10, 10, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 48, 48, 48, 48, 48, 49, 49, 49, 49, 10, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 276 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548380 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548380/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548380 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 681) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/681: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001489548380.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489548380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001489548380 none CC[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 39, 39, 46, 46, 46, 11, 11, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 50, 50, 50, 50, 50, 46, 46, 46, 46, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 306 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548380 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489548380 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548380/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548380/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489548380 Building ZINC001489564386 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564386' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564386 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489564386 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564386/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564386 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/682 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3[nH]ncc3c2)C[C@@H]1O) `ZINC001489564386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489564386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001489564386 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3[nH]ncc3c2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 151 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564386 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564386/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564386 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 683) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/683 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/683' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3[nH]ncc3c2)C[C@@H]1O) `ZINC001489564386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489564386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001489564386 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3[nH]ncc3c2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564386 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489564386 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564386/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564386/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564386 Building ZINC001489564386 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564386' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564386 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489564386 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564386/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564386 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 682) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/682: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3[nH]ncc3c2)C[C@@H]1O) `ZINC001489564386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489564386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001489564386 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3[nH]ncc3c2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 151 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564386 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564386/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564386 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 683) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/683: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3[nH]ncc3c2)C[C@@H]1O) `ZINC001489564386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489564386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001489564386 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cnc3[nH]ncc3c2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 8, 1, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564386 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489564386 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564386/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564386/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564386 Building ZINC001489564470 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564470' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564470 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489564470 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564470/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564470 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/684 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)N2CCOCC2)C[C@@H]1O) `ZINC001489564470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489564470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489564470 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)N2CCOCC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 6, 15, 15, 15, 15, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 45] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 230 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564470 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564470/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564470 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 685) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/685 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/685' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)N2CCOCC2)C[C@@H]1O) `ZINC001489564470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489564470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489564470 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)N2CCOCC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 5, 16, 16, 16, 16, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 48] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 229 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564470 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489564470 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564470/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564470/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564470 Building ZINC001489564470 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564470' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564470 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489564470 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564470/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564470 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 684) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/684: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)N2CCOCC2)C[C@@H]1O) `ZINC001489564470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489564470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489564470 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)N2CCOCC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 6, 15, 15, 15, 15, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 45] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 230 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564470 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564470/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564470 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 685) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/685: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)N2CCOCC2)C[C@@H]1O) `ZINC001489564470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489564470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489564470 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C(C)(C)N2CCOCC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 5, 16, 16, 16, 16, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 48] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 229 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564470 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489564470 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564470/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564470/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564470 Building ZINC001489564511 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564511' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564511 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489564511 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564511/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564511 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/686 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CC(=O)NCC2CC2)C[C@@H]1O) `ZINC001489564511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489564511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489564511 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CC(=O)NCC2CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 15, 31, 31, 31, 42, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 15, 31, 42, 42, 50, 50, 50, 50, 50, 3, 3, 9] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 36, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 205 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564511 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564511/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564511 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 687) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/687 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/687' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CC(=O)NCC2CC2)C[C@@H]1O) `ZINC001489564511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489564511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489564511 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CC(=O)NCC2CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 14, 34, 34, 34, 43, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 14, 14, 34, 43, 43, 50, 50, 50, 50, 50, 2, 2, 6] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 36, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564511 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489564511 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564511/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564511/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564511 Building ZINC001489564511 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564511' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564511 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489564511 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564511/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564511 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 686) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/686: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CC(=O)NCC2CC2)C[C@@H]1O) `ZINC001489564511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489564511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489564511 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CC(=O)NCC2CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 15, 31, 31, 31, 42, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 15, 31, 42, 42, 50, 50, 50, 50, 50, 3, 3, 9] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 36, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 205 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564511 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564511/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564511 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 687) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/687: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CC(=O)NCC2CC2)C[C@@H]1O) `ZINC001489564511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489564511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489564511 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CC(=O)NCC2CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 14, 34, 34, 34, 43, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 14, 14, 34, 43, 43, 50, 50, 50, 50, 50, 2, 2, 6] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 36, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564511 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489564511 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564511/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564511/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564511 Building ZINC001489564709 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564709' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564709 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489564709 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564709/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564709 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/688 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001489564709.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489564709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489564709 none Cn1cncc1[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 37, 37, 37, 37, 17, 37, 9, 17, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 37, 37, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 158 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564709 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564709/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564709 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 689) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/689 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/689' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001489564709.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489564709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564709/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489564709 none Cn1cncc1[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 36, 36, 36, 36, 18, 36, 10, 18, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 36, 36, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564709 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489564709 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564709/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564709/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564709 Building ZINC001489564709 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564709' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564709 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489564709 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564709/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564709 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 688) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/688: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001489564709.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489564709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489564709 none Cn1cncc1[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 37, 37, 37, 37, 17, 37, 9, 17, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 37, 37, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 158 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564709 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564709/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564709 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 689) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/689: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001489564709.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489564709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564709/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489564709 none Cn1cncc1[C@@H]1C[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 36, 36, 36, 36, 18, 36, 10, 18, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 36, 36, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564709 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489564709 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564709/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564709/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564709 Building ZINC001489564777 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564777' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564777 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489564777 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564777/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564777 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/690 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3ncnn32)C[C@@H]1O) `ZINC001489564777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489564777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001489564777 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3ncnn32)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 161 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564777 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564777/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564777 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 691) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/691 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/691' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3ncnn32)C[C@@H]1O) `ZINC001489564777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489564777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001489564777 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3ncnn32)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564777 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489564777 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564777/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564777/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564777 Building ZINC001489564777 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564777' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564777 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489564777 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564777/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564777 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 690) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/690: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3ncnn32)C[C@@H]1O) `ZINC001489564777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489564777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001489564777 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3ncnn32)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 161 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564777 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564777/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564777 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 691) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/691: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3ncnn32)C[C@@H]1O) `ZINC001489564777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489564777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001489564777 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3ncnn32)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564777 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489564777 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564777/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564777/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489564777 Building ZINC001489565063 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565063' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565063 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489565063 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565063/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565063 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/692 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CNC(=O)N2CCCC2)C[C@@H]1O) `ZINC001489565063.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489565063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001489565063 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CNC(=O)N2CCCC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 11, 37, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 212 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565063 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565063/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565063 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 693) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/693 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/693' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CNC(=O)N2CCCC2)C[C@@H]1O) `ZINC001489565063.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489565063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565063/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001489565063 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CNC(=O)N2CCCC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 12, 12, 36, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565063 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489565063 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565063/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565063/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565063 Building ZINC001489565063 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565063' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565063 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489565063 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565063/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565063 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 692) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/692: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CNC(=O)N2CCCC2)C[C@@H]1O) `ZINC001489565063.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489565063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001489565063 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CNC(=O)N2CCCC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 11, 37, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 212 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565063 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565063/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565063 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 693) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/693: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CNC(=O)N2CCCC2)C[C@@H]1O) `ZINC001489565063.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489565063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565063/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001489565063 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CNC(=O)N2CCCC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 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, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 12, 12, 36, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565063 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489565063 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565063/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565063/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565063 Building ZINC001489565068 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565068' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489565068 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565068/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/694 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1) `ZINC001489565068.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489565068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489565068 none CN(C)c1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 11, 25, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565068/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 695) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/695 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/695' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1) `ZINC001489565068.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489565068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489565068 none CN(C)c1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 10, 25, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489565068 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565068/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565068/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565068 Building ZINC001489565068 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565068' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489565068 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565068/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 694) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/694: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1) `ZINC001489565068.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489565068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489565068 none CN(C)c1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 11, 25, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565068/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 695) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/695: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1) `ZINC001489565068.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489565068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489565068 none CN(C)c1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 10, 25, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565068 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489565068 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565068/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565068/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565068 Building ZINC001489565202 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565202' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565202 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489565202 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565202/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565202 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/696 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCNC(=O)C2CC2)C[C@@H]1O) `ZINC001489565202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489565202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489565202 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCNC(=O)C2CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 13, 15, 22, 31, 31, 31, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 13, 13, 17, 17, 21, 21, 31, 50, 50, 50, 50, 50, 5, 5, 15] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 226 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565202 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565202/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565202 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 697) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/697 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/697' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCNC(=O)C2CC2)C[C@@H]1O) `ZINC001489565202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489565202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489565202 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCNC(=O)C2CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 12, 15, 23, 34, 34, 34, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 12, 17, 17, 22, 22, 34, 50, 50, 50, 50, 50, 3, 3, 9] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565202 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489565202 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565202/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565202/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565202 Building ZINC001489565202 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565202' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565202 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489565202 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565202/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565202 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 696) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/696: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCNC(=O)C2CC2)C[C@@H]1O) `ZINC001489565202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489565202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489565202 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCNC(=O)C2CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 13, 15, 22, 31, 31, 31, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 13, 13, 17, 17, 21, 21, 31, 50, 50, 50, 50, 50, 5, 5, 15] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 226 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565202 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565202/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565202 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 697) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/697: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCNC(=O)C2CC2)C[C@@H]1O) `ZINC001489565202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489565202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489565202 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCCNC(=O)C2CC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 12, 15, 23, 34, 34, 34, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 12, 17, 17, 22, 22, 34, 50, 50, 50, 50, 50, 3, 3, 9] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565202 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489565202 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565202/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565202/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565202 Building ZINC001489565231 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565231' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565231 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489565231 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565231/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565231 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/698 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1) `ZINC001489565231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489565231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489565231 none CO[C@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [33, 29, 12, 29, 8, 12, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 29, 50, 50, 50, 50, 50, 33, 33, 33, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 178 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565231 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565231/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565231 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 699) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/699 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/699' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1) `ZINC001489565231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489565231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489565231 none CO[C@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 28, 13, 28, 8, 13, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 28, 50, 50, 50, 50, 50, 34, 34, 34, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565231 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489565231 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565231/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565231/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565231 Building ZINC001489565231 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565231' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565231 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489565231 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565231/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565231 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 698) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/698: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1) `ZINC001489565231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489565231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489565231 none CO[C@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [33, 29, 12, 29, 8, 12, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 29, 50, 50, 50, 50, 50, 33, 33, 33, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 178 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565231 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565231/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565231 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 699) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/699: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1) `ZINC001489565231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489565231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489565231 none CO[C@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 28, 13, 28, 8, 13, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 28, 50, 50, 50, 50, 50, 34, 34, 34, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565231 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489565231 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565231/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565231/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565231 Building ZINC001489565232 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565232' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565232 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489565232 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565232/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565232 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/700 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1) `ZINC001489565232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489565232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489565232 none CO[C@@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [35, 30, 12, 30, 8, 12, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 30, 50, 50, 50, 50, 50, 35, 35, 35, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 183 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565232 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565232/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565232 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 701) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/701 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/701' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1) `ZINC001489565232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489565232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489565232 none CO[C@@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 32, 16, 32, 9, 16, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 32, 50, 50, 50, 50, 50, 38, 38, 38, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 185 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565232 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489565232 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565232/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565232/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565232 Building ZINC001489565232 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565232' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565232 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489565232 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565232/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565232 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 700) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/700: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1) `ZINC001489565232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489565232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489565232 none CO[C@@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [35, 30, 12, 30, 8, 12, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 30, 50, 50, 50, 50, 50, 35, 35, 35, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 183 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565232 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565232/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565232 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 701) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/701: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1) `ZINC001489565232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489565232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489565232 none CO[C@@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 32, 16, 32, 9, 16, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 32, 50, 50, 50, 50, 50, 38, 38, 38, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 185 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565232 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489565232 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565232/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565232/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565232 Building ZINC001489565253 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565253' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565253 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489565253 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565253/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565253 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/702 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cn3c(n2)COCC3)C[C@@H]1O) `ZINC001489565253.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489565253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001489565253 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cn3c(n2)COCC3)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 21, 21, 21, 21, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 21, 21, 50, 50, 50, 50, 50, 50, 50, 21, 21, 63] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 174 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565253 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565253/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565253 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 703) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/703 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/703' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cn3c(n2)COCC3)C[C@@H]1O) `ZINC001489565253.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489565253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565253/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001489565253 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cn3c(n2)COCC3)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 22, 22, 22, 22, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 22, 22, 50, 50, 50, 50, 50, 50, 50, 22, 22, 66] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565253 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489565253 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565253/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565253/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565253 Building ZINC001489565253 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565253' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565253 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489565253 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565253/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565253 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 702) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/702: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cn3c(n2)COCC3)C[C@@H]1O) `ZINC001489565253.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489565253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001489565253 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cn3c(n2)COCC3)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 21, 21, 21, 21, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 21, 21, 50, 50, 50, 50, 50, 50, 50, 21, 21, 63] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 174 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565253 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565253/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565253 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 703) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/703: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cn3c(n2)COCC3)C[C@@H]1O) `ZINC001489565253.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489565253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565253/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001489565253 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cn3c(n2)COCC3)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 22, 22, 22, 22, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 22, 22, 50, 50, 50, 50, 50, 50, 50, 22, 22, 66] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565253 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489565253 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565253/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565253/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565253 Building ZINC001489565258 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565258' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565258 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489565258 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565258/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565258 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/704 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCS(=O)(=O)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001489565258.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489565258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001489565258 none CCCS(=O)(=O)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 49, 28, 49, 49, 8, 5, 8, 5, 5, 3, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 28, 28, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565258 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565258/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565258 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 705) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/705 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/705' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCS(=O)(=O)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001489565258.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489565258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001489565258 none CCCS(=O)(=O)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 32, 50, 50, 11, 8, 11, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 32, 32, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 234 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565258 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489565258 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565258/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565258/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565258 Building ZINC001489565258 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565258' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565258 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489565258 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565258/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565258 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 704) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/704: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCS(=O)(=O)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001489565258.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489565258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001489565258 none CCCS(=O)(=O)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 49, 28, 49, 49, 8, 5, 8, 5, 5, 3, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 28, 28, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565258 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565258/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565258 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 705) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/705: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCS(=O)(=O)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001489565258.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489565258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001489565258 none CCCS(=O)(=O)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 32, 50, 50, 11, 8, 11, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 32, 32, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 234 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565258 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489565258 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565258/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565258/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565258 Building ZINC001489565270 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565270' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565270 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489565270 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565270/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565270 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/706 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ncn1) `ZINC001489565270.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489565270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001489565270 none COc1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 29, 13, 29, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46]) total number of confs: 154 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565270 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565270/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565270 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 707) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/707 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/707' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ncn1) `ZINC001489565270.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489565270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001489565270 none COc1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 28, 12, 28, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565270 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489565270 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565270/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565270/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565270 Building ZINC001489565270 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565270' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565270 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489565270 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565270/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565270 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 706) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/706: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ncn1) `ZINC001489565270.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489565270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001489565270 none COc1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 29, 13, 29, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46]) total number of confs: 154 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565270 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565270/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565270 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 707) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/707: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ncn1) `ZINC001489565270.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489565270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001489565270 none COc1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 28, 12, 28, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565270 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489565270 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565270/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565270/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565270 Building ZINC001489565395 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565395' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565395 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489565395 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565395/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565395 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/708 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc3ncccn3n2)C[C@@H]1O) `ZINC001489565395.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489565395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001489565395 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc3ncccn3n2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 1, 8, 1, 1, 1, 8, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 128 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565395 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565395/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565395 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 709) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/709 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/709' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc3ncccn3n2)C[C@@H]1O) `ZINC001489565395.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489565395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001489565395 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc3ncccn3n2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 1, 8, 1, 1, 1, 8, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565395 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489565395 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565395/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565395/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565395 Building ZINC001489565395 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565395' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565395 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489565395 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565395/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565395 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 708) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/708: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc3ncccn3n2)C[C@@H]1O) `ZINC001489565395.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489565395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001489565395 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc3ncccn3n2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 1, 8, 1, 1, 1, 8, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 128 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565395 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565395/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565395 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 709) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/709: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc3ncccn3n2)C[C@@H]1O) `ZINC001489565395.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489565395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001489565395 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2nc3ncccn3n2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 8, 1, 8, 1, 1, 1, 8, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565395 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489565395 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565395/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565395/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565395 Building ZINC001489565453 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565453' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565453 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489565453 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565453/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565453 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/710 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1C) `ZINC001489565453.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489565453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489565453 none CCc1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 27, 27, 27, 18, 9, 18, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 27, 27, 27, 50, 50, 50, 50, 50, 27, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 27, 27, 27] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565453 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565453/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565453 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 711) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/711 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/711' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1C) `ZINC001489565453.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489565453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489565453 none CCc1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 25, 25, 25, 17, 8, 17, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 25, 25, 25, 50, 50, 50, 50, 50, 25, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 25, 25, 25] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 237 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565453 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489565453 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565453/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565453/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565453 Building ZINC001489565453 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565453' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565453 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489565453 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565453/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565453 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 710) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/710: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1C) `ZINC001489565453.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489565453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489565453 none CCc1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 27, 27, 27, 18, 9, 18, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 27, 27, 27, 50, 50, 50, 50, 50, 27, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 27, 27, 27] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565453 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565453/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565453 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 711) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/711: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1C) `ZINC001489565453.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489565453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489565453 none CCc1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 25, 25, 25, 17, 8, 17, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 25, 25, 25, 50, 50, 50, 50, 50, 25, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 25, 25, 25] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50]) total number of confs: 237 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565453 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489565453 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565453/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565453/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565453 Building ZINC001489565483 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565483' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565483 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489565483 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565483/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565483 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/712 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nn(C)cc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001489565483.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489565483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001489565483 none COc1nn(C)cc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 26, 12, 26, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 147 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565483 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565483/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565483 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 713) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/713 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/713' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nn(C)cc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001489565483.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489565483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565483/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001489565483 none COc1nn(C)cc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 28, 12, 28, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565483 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489565483 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565483/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565483/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565483 Building ZINC001489565483 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565483' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565483 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489565483 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565483/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565483 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 712) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/712: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nn(C)cc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001489565483.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489565483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001489565483 none COc1nn(C)cc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 26, 12, 26, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 147 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565483 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565483/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565483 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 713) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/713: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nn(C)cc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001489565483.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489565483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565483/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001489565483 none COc1nn(C)cc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 28, 12, 28, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565483 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489565483 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565483/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565483/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565483 Building ZINC001489565732 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565732' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565732 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489565732 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565732/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565732 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/714 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccc1=O) `ZINC001489565732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489565732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001489565732 none CCn1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 36, 36, 36, 22, 12, 22, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 36, 36, 36, 36, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 36, 36] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565732 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565732/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565732 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 715) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/715 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/715' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccc1=O) `ZINC001489565732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489565732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001489565732 none CCn1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 29, 29, 29, 20, 11, 20, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 29, 29, 29, 29, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 29, 29] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 234 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565732 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489565732 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565732/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565732/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565732 Building ZINC001489565732 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565732' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565732 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489565732 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565732/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565732 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 714) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/714: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccc1=O) `ZINC001489565732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489565732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001489565732 none CCn1nc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 36, 36, 36, 22, 12, 22, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 36, 36, 36, 36, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 36, 36] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565732 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565732/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565732 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 715) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/715: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccc1=O) `ZINC001489565732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489565732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001489565732 none CCn1nc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)ccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 29, 29, 29, 20, 11, 20, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 29, 29, 29, 29, 50, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 29, 29] 150 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 234 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565732 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489565732 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565732/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565732/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565732 Building ZINC001489565961 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565961' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565961 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489565961 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565961/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565961 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/716 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncnc(O)c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001489565961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489565961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001489565961 none Cc1ncnc(O)c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 12, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 3, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 12, 32, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 100, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 300 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 261 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565961 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565961/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565961 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 717) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/717 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/717' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncnc(O)c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001489565961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489565961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001489565961 none Cc1ncnc(O)c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 12, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 3, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 33, 14, 33, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 100, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 300 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 265 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565961 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489565961 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565961/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565961/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565961 Building ZINC001489565961 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565961' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565961 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489565961 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565961/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565961 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 716) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/716: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncnc(O)c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001489565961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489565961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001489565961 none Cc1ncnc(O)c1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 12, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 3, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 32, 12, 32, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 100, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12] 300 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 261 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565961 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565961/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565961 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 717) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/717: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncnc(O)c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001489565961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489565961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001489565961 none Cc1ncnc(O)c1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 12, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 3, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 33, 14, 33, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 100, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 300 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 265 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565961 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489565961 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565961/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565961/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565961 Building ZINC001489565991 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565991' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565991 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489565991 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565991/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565991 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/718 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n(CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001489565991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489565991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489565991 none Cc1cc(C)n(CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 35, 11, 8, 11, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 183 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565991 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565991/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565991 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 719) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/719 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/719' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n(CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001489565991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489565991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489565991 none Cc1cc(C)n(CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 32, 9, 6, 9, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 168 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565991 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489565991 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565991/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565991/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565991 Building ZINC001489565991 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565991' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565991 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489565991 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565991/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565991 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 718) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/718: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n(CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001489565991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489565991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489565991 none Cc1cc(C)n(CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 35, 11, 8, 11, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 183 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565991 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565991/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565991 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 719) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/719: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n(CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001489565991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489565991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489565991 none Cc1cc(C)n(CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 32, 9, 6, 9, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 168 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565991 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489565991 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565991/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565991/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489565991 Building ZINC001489566022 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566022' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566022 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489566022 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566022/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566022 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/720 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1CCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001489566022.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489566022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489566022 none Cn1nccc1CCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 34, 34, 12, 8, 12, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 34, 34, 34, 34, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566022 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566022/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566022 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 721) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/721 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/721' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1CCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001489566022.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489566022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489566022 none Cn1nccc1CCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 32, 32, 15, 10, 15, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 32, 32, 32, 32, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566022 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489566022 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566022/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566022/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566022 Building ZINC001489566022 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566022' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566022 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489566022 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566022/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566022 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 720) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/720: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1CCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001489566022.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489566022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489566022 none Cn1nccc1CCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 34, 34, 12, 8, 12, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 34, 34, 34, 34, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566022 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566022/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566022 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 721) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/721: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1CCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001489566022.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489566022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489566022 none Cn1nccc1CCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 32, 32, 15, 10, 15, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 32, 32, 32, 32, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566022 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489566022 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566022/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566022/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566022 Building ZINC001489566079 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566079' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566079 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489566079 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566079/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566079 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/722 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3cncn3C2)C[C@@H]1O) `ZINC001489566079.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489566079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489566079 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3cncn3C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 25, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 170 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566079 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566079/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566079 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 723) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/723 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/723' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3cncn3C2)C[C@@H]1O) `ZINC001489566079.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489566079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489566079 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3cncn3C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 21, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 168 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566079 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489566079 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566079/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566079/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566079 Building ZINC001489566079 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566079' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566079 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489566079 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566079/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566079 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 722) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/722: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3cncn3C2)C[C@@H]1O) `ZINC001489566079.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489566079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489566079 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3cncn3C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 25, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 170 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566079 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566079/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566079 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 723) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/723: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3cncn3C2)C[C@@H]1O) `ZINC001489566079.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489566079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489566079 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3cncn3C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 21, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 168 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566079 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489566079 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566079/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566079/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566079 Building ZINC001489566080 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566080' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566080 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489566080 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566080/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566080 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/724 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3cncn3C2)C[C@@H]1O) `ZINC001489566080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489566080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489566080 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3cncn3C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 24, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 166 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566080 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566080/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566080 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 725) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/725 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/725' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3cncn3C2)C[C@@H]1O) `ZINC001489566080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489566080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489566080 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3cncn3C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 26, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 176 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566080 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489566080 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566080/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566080/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566080 Building ZINC001489566080 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566080' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566080 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489566080 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566080/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566080 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 724) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/724: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3cncn3C2)C[C@@H]1O) `ZINC001489566080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489566080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489566080 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3cncn3C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 24, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 166 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566080 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566080/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566080 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 725) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/725: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3cncn3C2)C[C@@H]1O) `ZINC001489566080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489566080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001489566080 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3cncn3C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 1, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 26, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 176 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566080 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489566080 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566080/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566080/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489566080 Building ZINC001489578623 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489578623' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489578623 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489578623 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489578623/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489578623 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/726 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)NCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001489578623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489578623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489578623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001489578623 none CC(C)(C)C(=O)NCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 49, 17, 17, 17, 9, 9, 9, 9, 6, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 17, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 27] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489578623 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489578623/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489578623 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 727) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/727 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/727' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)NCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001489578623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489578623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489578623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001489578623 none CC(C)(C)C(=O)NCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 35, 11, 11, 11, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489578623 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489578623 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489578623/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489578623/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489578623 Building ZINC001489578623 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489578623' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489578623 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489578623 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489578623/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489578623 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 726) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/726: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)NCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001489578623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489578623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489578623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001489578623 none CC(C)(C)C(=O)NCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 49, 17, 17, 17, 9, 9, 9, 9, 6, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 17, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 27] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489578623 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489578623/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489578623 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 727) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/727: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)NCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001489578623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489578623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489578623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001489578623 none CC(C)(C)C(=O)NCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 35, 11, 11, 11, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489578623 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489578623 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489578623/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489578623/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489578623 Building ZINC001489589164 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489589164' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489589164 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489589164 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489589164/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489589164 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/728 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCCNC(=O)C2CC2)[C@@H](O)C1) `ZINC001489589164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489589164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489589164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489589164 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCCNC(=O)C2CC2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 4, 4, 4, 14, 18, 19, 32, 32, 32, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 18, 18, 19, 19, 32, 50, 50, 50, 50, 50, 6, 2, 2] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 202 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489589164 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489589164/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489589164 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 729) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/729 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/729' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCCNC(=O)C2CC2)[C@@H](O)C1) `ZINC001489589164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489589164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489589164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489589164 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCCNC(=O)C2CC2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 8, 8, 8, 25, 22, 33, 39, 39, 39, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 25, 25, 29, 29, 29, 30, 39, 50, 50, 50, 50, 50, 12, 4, 4] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 238 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489589164 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489589164 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489589164/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489589164/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489589164 Building ZINC001489589164 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489589164' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489589164 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489589164 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489589164/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489589164 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 728) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/728: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCCNC(=O)C2CC2)[C@@H](O)C1) `ZINC001489589164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489589164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489589164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489589164 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCCNC(=O)C2CC2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 4, 4, 4, 14, 18, 19, 32, 32, 32, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 18, 18, 19, 19, 32, 50, 50, 50, 50, 50, 6, 2, 2] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 202 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489589164 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489589164/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489589164 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 729) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/729: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCCNC(=O)C2CC2)[C@@H](O)C1) `ZINC001489589164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489589164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489589164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001489589164 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCCNC(=O)C2CC2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 8, 8, 8, 25, 22, 33, 39, 39, 39, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 25, 25, 29, 29, 29, 30, 39, 50, 50, 50, 50, 50, 12, 4, 4] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 238 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489589164 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489589164 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489589164/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489589164/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489589164 Building ZINC001489601766 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489601766' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489601766 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489601766 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489601766/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489601766 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/730 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCN2CCOCC2)[C@@H](O)C1) `ZINC001489601766.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489601766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489601766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001489601766 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCN2CCOCC2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 5, 8, 8, 8, 8, 13, 13, 13, 32, 32, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 13, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 24, 8, 8] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 175 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489601766 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489601766/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489601766 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 731) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/731 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/731' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCN2CCOCC2)[C@@H](O)C1) `ZINC001489601766.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489601766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489601766/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001489601766 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCN2CCOCC2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 6, 6, 6, 6, 11, 11, 11, 30, 30, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 11, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 18, 6, 6] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489601766 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489601766 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489601766/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489601766/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489601766 Building ZINC001489601766 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489601766' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489601766 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489601766 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489601766/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489601766 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 730) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/730: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCN2CCOCC2)[C@@H](O)C1) `ZINC001489601766.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489601766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489601766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001489601766 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCN2CCOCC2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 5, 8, 8, 8, 8, 13, 13, 13, 32, 32, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 13, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 24, 8, 8] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 175 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489601766 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489601766/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489601766 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 731) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/731: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCN2CCOCC2)[C@@H](O)C1) `ZINC001489601766.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489601766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489601766/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001489601766 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCN2CCOCC2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 10, 5, 5, 12, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 6, 6, 6, 6, 11, 11, 11, 30, 30, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 11, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 18, 6, 6] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489601766 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489601766 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489601766/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489601766/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489601766 Building ZINC001489605012 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605012' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605012 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489605012 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605012/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605012 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/732 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001489605012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489605012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001489605012 none CC(C)NC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 43, 50, 27, 27, 13, 13, 13, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 33, 33, 27, 27, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 253 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605012 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605012/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605012 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 733) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/733 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/733' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001489605012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489605012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001489605012 none CC(C)NC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 48, 50, 37, 34, 14, 14, 14, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 47, 48, 41, 41, 34, 34, 14, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 24] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 254 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605012 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489605012 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605012/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605012/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605012 Building ZINC001489605012 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605012' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605012 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489605012 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605012/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605012 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 732) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/732: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001489605012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489605012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001489605012 none CC(C)NC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 43, 50, 27, 27, 13, 13, 13, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 33, 33, 27, 27, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 253 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605012 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605012/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605012 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 733) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/733: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001489605012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489605012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001489605012 none CC(C)NC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 48, 50, 37, 34, 14, 14, 14, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 47, 48, 41, 41, 34, 34, 14, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 24] 150 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 254 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605012 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489605012 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605012/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605012/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605012 Building ZINC001489605441 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605441' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605441 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489605441 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605441/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605441 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/734 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O)c1cnn(C)c1) `ZINC001489605441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489605441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489605441 none CO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 26, 13, 26, 13, 13, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 26, 50, 50, 50, 50, 50, 27, 27, 27, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605441 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605441/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605441 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 735) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/735 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/735' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O)c1cnn(C)c1) `ZINC001489605441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489605441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489605441 none CO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 15, 28, 15, 15, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 28, 50, 50, 50, 50, 50, 28, 28, 28, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605441 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489605441 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605441/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605441/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605441 Building ZINC001489605441 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605441' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605441 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489605441 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605441/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605441 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 734) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/734: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O)c1cnn(C)c1) `ZINC001489605441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489605441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489605441 none CO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 26, 13, 26, 13, 13, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 26, 50, 50, 50, 50, 50, 27, 27, 27, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605441 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605441/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605441 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 735) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/735: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O)c1cnn(C)c1) `ZINC001489605441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489605441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489605441 none CO[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 15, 28, 15, 15, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 28, 50, 50, 50, 50, 50, 28, 28, 28, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605441 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489605441 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605441/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605441/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605441 Building ZINC001489605442 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605442' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605442 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489605442 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605442/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605442 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/736 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O)c1cnn(C)c1) `ZINC001489605442.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489605442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489605442 none CO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 19, 35, 19, 19, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 35, 50, 50, 50, 50, 50, 35, 35, 35, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605442 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605442/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605442 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 737) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/737 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/737' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O)c1cnn(C)c1) `ZINC001489605442.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489605442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489605442 none CO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 30, 14, 30, 14, 14, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 30, 50, 50, 50, 50, 50, 31, 31, 31, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605442 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489605442 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605442/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605442/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605442 Building ZINC001489605442 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605442' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605442 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489605442 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605442/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605442 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 736) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/736: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O)c1cnn(C)c1) `ZINC001489605442.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489605442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489605442 none CO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 19, 35, 19, 19, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 35, 50, 50, 50, 50, 50, 35, 35, 35, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605442 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605442/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605442 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 737) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/737: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O)c1cnn(C)c1) `ZINC001489605442.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489605442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489605442 none CO[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [31, 30, 14, 30, 14, 14, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 30, 50, 50, 50, 50, 50, 31, 31, 31, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 50, 50, 50, 50, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605442 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489605442 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605442/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605442/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489605442 Building ZINC001489925675 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489925675' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489925675 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489925675 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489925675/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489925675 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/738 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1cnnn1) `ZINC001489925675.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489925675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489925675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489925675 none CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1cnnn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', '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, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 9, 21, 21, 21, 43, 50, 50, 50, 50, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 9, 21, 43, 43, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489925675 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489925675/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489925675 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 739) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/739 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/739' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1cnnn1) `ZINC001489925675.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489925675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489925675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489925675 none CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1cnnn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', '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, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 21, 21, 21, 41, 50, 50, 50, 50, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 21, 41, 41, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489925675 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489925675 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489925675/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489925675/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489925675 Building ZINC001489925675 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489925675' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489925675 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489925675 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489925675/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489925675 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 738) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/738: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1cnnn1) `ZINC001489925675.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489925675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489925675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489925675 none CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1cnnn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', '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, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 9, 21, 21, 21, 43, 50, 50, 50, 50, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 9, 21, 43, 43, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489925675 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489925675/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489925675 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 739) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/739: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1cnnn1) `ZINC001489925675.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489925675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489925675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489925675 none CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1cnnn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', '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, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 21, 21, 21, 41, 50, 50, 50, 50, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 21, 41, 41, 50] 50 rigid atoms, others: [35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 43, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489925675 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489925675 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489925675/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489925675/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489925675 Building ZINC001489989339 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489989339' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489989339 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489989339 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489989339/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489989339 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/740 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN1CC(=O)NC1=O) `ZINC001489989339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489989339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489989339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489989339 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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: [9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 15, 15, 35, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 35, 35, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 148 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489989339 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489989339/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489989339 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 741) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/741 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/741' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN1CC(=O)NC1=O) `ZINC001489989339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489989339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489989339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489989339 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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: [9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 15, 15, 40, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 40, 40, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489989339 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489989339 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489989339/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489989339/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489989339 Building ZINC001489989339 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489989339' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489989339 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489989339 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489989339/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489989339 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 740) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/740: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN1CC(=O)NC1=O) `ZINC001489989339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489989339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489989339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489989339 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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: [9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 15, 15, 35, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 35, 35, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 148 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489989339 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489989339/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489989339 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 741) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/741: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN1CC(=O)NC1=O) `ZINC001489989339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489989339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489989339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001489989339 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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: [9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 15, 15, 40, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 40, 40, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489989339 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489989339 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489989339/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489989339/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489989339 Building ZINC001489990202 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489990202' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489990202 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489990202 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489990202/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489990202 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/742 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cn1c(O)nnc1O) `ZINC001489990202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489990202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489990202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489990202 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cn1c(O)nnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'O.3', 'N.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 12, 8, 8, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 22, 22, 43, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 43, 43, 150, 150] 450 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 462 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489990202 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489990202/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489990202 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 743) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/743 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/743' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cn1c(O)nnc1O) `ZINC001489990202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489990202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489990202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489990202 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cn1c(O)nnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'O.3', 'N.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 12, 8, 8, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [13, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 21, 21, 42, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 42, 42, 150, 150] 450 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 485 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489990202 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489990202 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489990202/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489990202/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489990202 Building ZINC001489990202 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489990202' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489990202 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001489990202 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489990202/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489990202 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 742) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/742: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cn1c(O)nnc1O) `ZINC001489990202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001489990202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489990202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489990202 none CC[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cn1c(O)nnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'O.3', 'N.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 12, 8, 8, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 22, 22, 43, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 43, 43, 150, 150] 450 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 462 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489990202 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489990202/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489990202 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 743) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/743: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cn1c(O)nnc1O) `ZINC001489990202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001489990202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489990202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001489990202 none CC[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cn1c(O)nnc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'O.3', 'N.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 12, 8, 8, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [13, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 21, 21, 42, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 42, 42, 150, 150] 450 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 485 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489990202 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001489990202 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489990202/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489990202/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001489990202 Building ZINC001490081933 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081933' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001490081933 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081933/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/744 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N[C@@H](C)C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001490081933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001490081933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001490081933 none COCC(=O)N[C@@H](C)C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 32, 32, 28, 12, 28, 28, 10, 12, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 50, 50, 50, 50, 50, 32, 28, 28, 28, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081933/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 745) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/745 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/745' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N[C@@H](C)C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001490081933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001490081933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001490081933 none COCC(=O)N[C@@H](C)C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 31, 31, 31, 27, 13, 27, 27, 10, 13, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 50, 50, 50, 50, 50, 31, 27, 27, 27, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001490081933 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081933/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081933/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081933 Building ZINC001490081933 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081933' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001490081933 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081933/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 744) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/744: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N[C@@H](C)C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001490081933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001490081933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001490081933 none COCC(=O)N[C@@H](C)C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 32, 32, 28, 12, 28, 28, 10, 12, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 50, 50, 50, 50, 50, 32, 28, 28, 28, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081933/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 745) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/745: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N[C@@H](C)C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001490081933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001490081933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001490081933 none COCC(=O)N[C@@H](C)C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 31, 31, 31, 27, 13, 27, 27, 10, 13, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 50, 50, 50, 50, 50, 31, 27, 27, 27, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081933 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001490081933 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081933/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081933/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081933 Building ZINC001490081935 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081935' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081935 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001490081935 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081935/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081935 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/746 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N[C@H](C)C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001490081935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001490081935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001490081935 none COCC(=O)N[C@H](C)C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 26, 26, 26, 20, 12, 20, 20, 9, 12, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 50, 50, 50, 50, 26, 20, 20, 20, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081935 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081935/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081935 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 747) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/747 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/747' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N[C@H](C)C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001490081935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001490081935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001490081935 none COCC(=O)N[C@H](C)C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 28, 28, 28, 22, 13, 22, 22, 11, 13, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 50, 50, 50, 50, 28, 22, 22, 22, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081935 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001490081935 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081935/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081935/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081935 Building ZINC001490081935 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081935' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081935 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001490081935 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081935/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081935 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 746) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/746: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N[C@H](C)C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001490081935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001490081935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001490081935 none COCC(=O)N[C@H](C)C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 26, 26, 26, 20, 12, 20, 20, 9, 12, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 50, 50, 50, 50, 26, 20, 20, 20, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081935 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081935/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081935 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 747) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/747: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N[C@H](C)C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001490081935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001490081935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001490081935 none COCC(=O)N[C@H](C)C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 28, 28, 28, 22, 13, 22, 22, 11, 13, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 50, 50, 50, 50, 28, 22, 22, 22, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081935 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001490081935 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081935/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081935/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490081935 Building ZINC001490091583 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091583' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091583 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001490091583 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091583/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091583 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/748 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CC[C@H]2NC(=O)NC2=O)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001490091583.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001490091583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001490091583 none C[C@@H]1[C@@H](NC(=O)CC[C@H]2NC(=O)NC2=O)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 5, 7, 8, 1, 11, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 8, 43, 33, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 43, 43, 47, 47, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091583 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091583/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091583 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 749) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/749 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/749' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CC[C@H]2NC(=O)NC2=O)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001490091583.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001490091583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091583/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001490091583 none C[C@@H]1[C@@H](NC(=O)CC[C@H]2NC(=O)NC2=O)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 5, 7, 8, 1, 11, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 10, 10, 38, 34, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 38, 38, 44, 44, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091583 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001490091583 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091583/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091583/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091583 Building ZINC001490091583 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091583' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091583 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001490091583 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091583/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091583 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 748) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/748: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CC[C@H]2NC(=O)NC2=O)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001490091583.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001490091583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001490091583 none C[C@@H]1[C@@H](NC(=O)CC[C@H]2NC(=O)NC2=O)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 5, 7, 8, 1, 11, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 8, 43, 33, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 43, 43, 47, 47, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091583 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091583/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091583 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 749) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/749: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CC[C@H]2NC(=O)NC2=O)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001490091583.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001490091583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091583/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001490091583 none C[C@@H]1[C@@H](NC(=O)CC[C@H]2NC(=O)NC2=O)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 5, 7, 8, 1, 11, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 10, 10, 38, 34, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 38, 38, 44, 44, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091583 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001490091583 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091583/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091583/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091583 Building ZINC001490091584 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091584' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091584 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001490091584 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091584/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091584 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/750 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CC[C@@H]2NC(=O)NC2=O)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001490091584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001490091584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001490091584 none C[C@@H]1[C@@H](NC(=O)CC[C@@H]2NC(=O)NC2=O)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 5, 7, 8, 1, 11, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 8, 42, 31, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 42, 42, 47, 47, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091584 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091584/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091584 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 751) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/751 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/751' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CC[C@@H]2NC(=O)NC2=O)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001490091584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001490091584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001490091584 none C[C@@H]1[C@@H](NC(=O)CC[C@@H]2NC(=O)NC2=O)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 5, 7, 8, 1, 11, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 10, 10, 34, 32, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 34, 34, 44, 44, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091584 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001490091584 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091584/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091584/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091584 Building ZINC001490091584 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091584' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091584 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001490091584 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091584/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091584 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 750) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/750: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CC[C@@H]2NC(=O)NC2=O)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001490091584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001490091584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001490091584 none C[C@@H]1[C@@H](NC(=O)CC[C@@H]2NC(=O)NC2=O)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 5, 7, 8, 1, 11, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 8, 42, 31, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 42, 42, 47, 47, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091584 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091584/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091584 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 751) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/751: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CC[C@@H]2NC(=O)NC2=O)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001490091584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001490091584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001490091584 none C[C@@H]1[C@@H](NC(=O)CC[C@@H]2NC(=O)NC2=O)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 5, 7, 8, 1, 11, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 10, 10, 34, 32, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 34, 34, 44, 44, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091584 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001490091584 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091584/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091584/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490091584 Building ZINC001490112522 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490112522' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490112522 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001490112522 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490112522/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490112522 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/752 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CCn2ncn(C)c2=O)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001490112522.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001490112522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490112522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001490112522 none C[C@@H]1[C@@H](NC(=O)CCn2ncn(C)c2=O)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 8, 8, 1, 8, 5, 1, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 36, 40, 50, 50, 50, 50, 50, 50, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 36, 36, 40, 40, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 171 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490112522 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490112522/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490112522 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 753) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/753 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/753' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CCn2ncn(C)c2=O)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001490112522.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001490112522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490112522/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001490112522 none C[C@@H]1[C@@H](NC(=O)CCn2ncn(C)c2=O)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 8, 8, 1, 8, 5, 1, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 37, 42, 50, 50, 50, 50, 50, 50, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 37, 37, 42, 42, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490112522 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001490112522 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490112522/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490112522/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490112522 Building ZINC001490112522 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490112522' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490112522 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001490112522 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490112522/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490112522 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 752) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/752: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CCn2ncn(C)c2=O)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001490112522.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001490112522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490112522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001490112522 none C[C@@H]1[C@@H](NC(=O)CCn2ncn(C)c2=O)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 8, 8, 1, 8, 5, 1, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 36, 40, 50, 50, 50, 50, 50, 50, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 36, 36, 40, 40, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 171 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490112522 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490112522/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490112522 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 753) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/753: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)CCn2ncn(C)c2=O)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001490112522.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001490112522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490112522/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001490112522 none C[C@@H]1[C@@H](NC(=O)CCn2ncn(C)c2=O)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 8, 8, 1, 8, 5, 1, 11, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 37, 42, 50, 50, 50, 50, 50, 50, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 37, 37, 42, 42, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490112522 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001490112522 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490112522/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490112522/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490112522 Building ZINC001490210769 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490210769' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490210769 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001490210769 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490210769/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490210769 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/754 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/754' -> `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]2CN(C(=O)CCNC(N)=O)C[C@@]2(C)C1) `ZINC001490210769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001490210769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490210769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001490210769 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)CCNC(N)=O)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 6, 6, 6, 6, 6, 6, 10, 10, 25, 41, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 25, 25, 41, 41, 50, 50, 50, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490210769 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490210769/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490210769 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 755) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/755 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/755' -> `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]2CN(C(=O)CCNC(N)=O)C[C@@]2(C)C1) `ZINC001490210769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001490210769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490210769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001490210769 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)CCNC(N)=O)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 6, 6, 6, 6, 6, 6, 10, 10, 25, 42, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 25, 25, 42, 42, 50, 50, 50, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490210769 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001490210769 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490210769/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490210769/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490210769 Building ZINC001490210769 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490210769' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490210769 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001490210769 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490210769/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490210769 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 754) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/754: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)CCNC(N)=O)C[C@@]2(C)C1) `ZINC001490210769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001490210769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490210769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001490210769 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)CCNC(N)=O)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 6, 6, 6, 6, 6, 6, 10, 10, 25, 41, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 25, 25, 41, 41, 50, 50, 50, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490210769 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490210769/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490210769 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 755) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/755: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)CCNC(N)=O)C[C@@]2(C)C1) `ZINC001490210769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001490210769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490210769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001490210769 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C(=O)CCNC(N)=O)C[C@@]2(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 6, 6, 6, 6, 6, 6, 10, 10, 25, 42, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 25, 25, 42, 42, 50, 50, 50, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490210769 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001490210769 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490210769/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490210769/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490210769 Building ZINC001490274632 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490274632' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490274632 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001490274632 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490274632/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490274632 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/756 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CN2C(=O)CNC2=O)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001490274632.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001490274632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490274632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001490274632 none C[C@@H]1CN(C(=O)CN2C(=O)CNC2=O)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 29, 50, 50, 50, 50, 50, 50, 26, 15, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 29, 29, 50, 50, 50, 26, 26, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490274632 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490274632/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490274632 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 757) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/757 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/757' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CN2C(=O)CNC2=O)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001490274632.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001490274632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490274632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001490274632 none C[C@@H]1CN(C(=O)CN2C(=O)CNC2=O)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 28, 28, 31, 50, 50, 50, 50, 50, 50, 27, 17, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 31, 31, 50, 50, 50, 27, 27, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490274632 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001490274632 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490274632/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490274632/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490274632 Building ZINC001490274632 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490274632' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490274632 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001490274632 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490274632/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490274632 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 756) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/756: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CN2C(=O)CNC2=O)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001490274632.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001490274632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490274632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001490274632 none C[C@@H]1CN(C(=O)CN2C(=O)CNC2=O)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 29, 50, 50, 50, 50, 50, 50, 26, 15, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 29, 29, 50, 50, 50, 26, 26, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490274632 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490274632/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490274632 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 757) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/757: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CN2C(=O)CNC2=O)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001490274632.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001490274632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490274632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001490274632 none C[C@@H]1CN(C(=O)CN2C(=O)CNC2=O)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 28, 28, 31, 50, 50, 50, 50, 50, 50, 27, 17, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 31, 31, 50, 50, 50, 27, 27, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490274632 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001490274632 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490274632/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490274632/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490274632 Building ZINC001490276145 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490276145' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490276145 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001490276145 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490276145/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490276145 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/758 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N(C)CC(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001490276145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001490276145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490276145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001490276145 none COCC(=O)N(C)CC(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 37, 37, 29, 37, 17, 17, 17, 17, 17, 10, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 50, 50, 50, 50, 50, 37, 37, 37, 29, 29, 17, 17, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490276145 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490276145/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490276145 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 759) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/759 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/759' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N(C)CC(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001490276145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001490276145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490276145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001490276145 none COCC(=O)N(C)CC(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 32, 32, 29, 32, 17, 17, 17, 17, 17, 13, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 50, 50, 50, 50, 50, 32, 32, 32, 29, 29, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490276145 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001490276145 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490276145/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490276145/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490276145 Building ZINC001490276145 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490276145' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490276145 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001490276145 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490276145/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490276145 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 758) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/758: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N(C)CC(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001490276145.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001490276145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490276145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001490276145 none COCC(=O)N(C)CC(=O)N1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 37, 37, 29, 37, 17, 17, 17, 17, 17, 10, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 50, 50, 50, 50, 50, 37, 37, 37, 29, 29, 17, 17, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490276145 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490276145/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490276145 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 759) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/759: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N(C)CC(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC001490276145.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001490276145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490276145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001490276145 none COCC(=O)N(C)CC(=O)N1C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 32, 32, 29, 32, 17, 17, 17, 17, 17, 13, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 50, 50, 50, 50, 50, 32, 32, 32, 29, 29, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54, 55, 56]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490276145 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001490276145 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490276145/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490276145/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490276145 Building ZINC001490541156 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541156' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541156 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001490541156 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541156/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541156 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/760 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCO[C@@](C)(CNC(=O)[C@H]2C[C@H]2C(N)=O)C1) `ZINC001490541156.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001490541156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001490541156 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCO[C@@](C)(CNC(=O)[C@H]2C[C@H]2C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 4, 5, 6, 6, 6, 6, 6, 6, 17, 28, 28, 28, 49, 49, 49, 49, 49, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 17, 17, 28, 49, 49, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541156 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541156/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541156 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 761) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/761 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/761' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCO[C@@](C)(CNC(=O)[C@H]2C[C@H]2C(N)=O)C1) `ZINC001490541156.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001490541156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541156/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001490541156 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCO[C@@](C)(CNC(=O)[C@H]2C[C@H]2C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 5, 5, 14, 27, 27, 27, 48, 48, 48, 48, 48, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 14, 14, 27, 48, 48, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541156 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001490541156 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541156/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541156/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541156 Building ZINC001490541156 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541156' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541156 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001490541156 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541156/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541156 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 760) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/760: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCO[C@@](C)(CNC(=O)[C@H]2C[C@H]2C(N)=O)C1) `ZINC001490541156.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001490541156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001490541156 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCO[C@@](C)(CNC(=O)[C@H]2C[C@H]2C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 4, 5, 6, 6, 6, 6, 6, 6, 17, 28, 28, 28, 49, 49, 49, 49, 49, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 17, 17, 28, 49, 49, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541156 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541156/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541156 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 761) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/761: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCO[C@@](C)(CNC(=O)[C@H]2C[C@H]2C(N)=O)C1) `ZINC001490541156.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001490541156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541156/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001490541156 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCO[C@@](C)(CNC(=O)[C@H]2C[C@H]2C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 5, 5, 14, 27, 27, 27, 48, 48, 48, 48, 48, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 14, 14, 27, 48, 48, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541156 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001490541156 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541156/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541156/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541156 Building ZINC001490541159 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541159' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541159 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001490541159 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541159/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541159 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/762 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCO[C@](C)(CNC(=O)[C@H]2C[C@H]2C(N)=O)C1) `ZINC001490541159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001490541159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001490541159 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCO[C@](C)(CNC(=O)[C@H]2C[C@H]2C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 4, 6, 7, 7, 7, 7, 7, 7, 18, 26, 26, 26, 48, 48, 48, 48, 48, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 18, 18, 26, 48, 48, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541159 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541159/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541159 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 763) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/763 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/763' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCO[C@](C)(CNC(=O)[C@H]2C[C@H]2C(N)=O)C1) `ZINC001490541159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001490541159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001490541159 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCO[C@](C)(CNC(=O)[C@H]2C[C@H]2C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 4, 6, 8, 8, 8, 8, 8, 8, 18, 31, 31, 31, 45, 45, 45, 45, 45, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 18, 18, 31, 45, 45, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541159 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001490541159 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541159/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541159/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541159 Building ZINC001490541159 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541159' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541159 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001490541159 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541159/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541159 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 762) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/762: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCO[C@](C)(CNC(=O)[C@H]2C[C@H]2C(N)=O)C1) `ZINC001490541159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001490541159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001490541159 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCO[C@](C)(CNC(=O)[C@H]2C[C@H]2C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 4, 6, 7, 7, 7, 7, 7, 7, 18, 26, 26, 26, 48, 48, 48, 48, 48, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 18, 18, 26, 48, 48, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541159 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541159/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541159 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 763) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/763: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCO[C@](C)(CNC(=O)[C@H]2C[C@H]2C(N)=O)C1) `ZINC001490541159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001490541159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001490541159 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCO[C@](C)(CNC(=O)[C@H]2C[C@H]2C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 4, 6, 8, 8, 8, 8, 8, 8, 18, 31, 31, 31, 45, 45, 45, 45, 45, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 18, 18, 31, 45, 45, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541159 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001490541159 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541159/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541159/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490541159 Building ZINC001490578694 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490578694' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490578694 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001490578694 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490578694/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490578694 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/764 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/764' -> `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]1C[C@H]2CC[C@@H]1N2C(=O)CCNS(C)(=O)=O) `ZINC001490578694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001490578694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490578694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001490578694 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)CCNS(C)(=O)=O NO_LONG_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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 23, 45, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 17, 17, 23, 23, 45, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490578694 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490578694/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490578694 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 765) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/765 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/765' -> `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]1C[C@H]2CC[C@@H]1N2C(=O)CCNS(C)(=O)=O) `ZINC001490578694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001490578694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490578694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001490578694 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)CCNS(C)(=O)=O NO_LONG_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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 21, 24, 46, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 21, 21, 24, 24, 46, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490578694 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001490578694 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490578694/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490578694/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490578694 Building ZINC001490578694 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490578694' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490578694 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001490578694 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490578694/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490578694 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 764) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/764: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)CCNS(C)(=O)=O) `ZINC001490578694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001490578694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490578694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001490578694 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)CCNS(C)(=O)=O NO_LONG_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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 23, 45, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 17, 17, 23, 23, 45, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490578694 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490578694/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490578694 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 765) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/765: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)CCNS(C)(=O)=O) `ZINC001490578694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001490578694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490578694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001490578694 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)CCNS(C)(=O)=O NO_LONG_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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 21, 24, 46, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 21, 21, 24, 24, 46, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490578694 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001490578694 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490578694/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490578694/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490578694 Building ZINC001490579623 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490579623' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490579623 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001490579623 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490579623/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490579623 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/766 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)CC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001490579623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001490579623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490579623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001490579623 none CNS(=O)(=O)CC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 30, 50, 50, 9, 6, 9, 6, 6, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 30, 30, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 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, 47, 48]) total number of confs: 208 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490579623 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490579623/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490579623 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 767) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/767 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/767' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)CC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001490579623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001490579623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490579623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001490579623 none CNS(=O)(=O)CC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 34, 50, 50, 11, 8, 11, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 34, 34, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 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, 47, 48]) total number of confs: 213 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490579623 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001490579623 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490579623/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490579623/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490579623 Building ZINC001490579623 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490579623' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490579623 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001490579623 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490579623/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490579623 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 766) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/766: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)CC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001490579623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001490579623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490579623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001490579623 none CNS(=O)(=O)CC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 30, 50, 50, 9, 6, 9, 6, 6, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 30, 30, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 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, 47, 48]) total number of confs: 208 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490579623 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490579623/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490579623 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 767) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/767: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)CC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001490579623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001490579623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490579623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001490579623 none CNS(=O)(=O)CC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 34, 50, 50, 11, 8, 11, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 34, 34, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 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, 47, 48]) total number of confs: 213 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490579623 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001490579623 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490579623/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490579623/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001490579623 Building ZINC001492018307 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018307' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018307 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001492018307 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018307/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018307 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/768 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001492018307.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001492018307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001492018307 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 11, 11, 11, 11, 11, 21, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 36, 38, 37, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018307 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018307/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018307 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 769) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/769 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/769' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001492018307.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001492018307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001492018307 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 10, 10, 10, 10, 10, 20, 27, 49, 49, 49, 49, 49, 49, 50, 50, 49, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 49, 49, 49, 49, 50, 50, 10, 10] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 36, 38, 37, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018307 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001492018307 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018307/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018307/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018307 Building ZINC001492018307 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018307' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018307 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001492018307 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018307/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018307 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 768) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/768: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001492018307.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001492018307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001492018307 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 11, 11, 11, 11, 11, 21, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 36, 38, 37, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018307 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018307/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018307 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 769) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/769: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001492018307.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001492018307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001492018307 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 10, 10, 10, 10, 10, 20, 27, 49, 49, 49, 49, 49, 49, 50, 50, 49, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 49, 49, 49, 49, 50, 50, 10, 10] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 36, 38, 37, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018307 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001492018307 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018307/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018307/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018307 Building ZINC001492018310 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018310' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018310 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001492018310 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018310/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018310 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/770 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001492018310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001492018310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001492018310 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 10, 10, 10, 10, 10, 21, 28, 49, 49, 49, 49, 49, 49, 50, 50, 49, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 49, 49, 49, 49, 50, 50, 10, 10] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 36, 38, 37, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 132 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018310 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018310/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018310 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 771) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/771 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/771' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001492018310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001492018310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001492018310 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 12, 12, 19, 24, 49, 49, 49, 49, 49, 49, 50, 50, 49, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 49, 49, 49, 49, 50, 50, 12, 12] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 36, 38, 37, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018310 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001492018310 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018310/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018310/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018310 Building ZINC001492018310 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018310' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018310 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001492018310 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018310/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018310 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 770) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/770: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001492018310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001492018310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001492018310 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 10, 10, 10, 10, 10, 21, 28, 49, 49, 49, 49, 49, 49, 50, 50, 49, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 49, 49, 49, 49, 50, 50, 10, 10] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 36, 38, 37, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 132 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018310 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018310/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018310 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 771) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/771: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001492018310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001492018310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001492018310 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 12, 12, 19, 24, 49, 49, 49, 49, 49, 49, 50, 50, 49, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 49, 49, 49, 49, 50, 50, 12, 12] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 36, 38, 37, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018310 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001492018310 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018310/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018310/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001492018310 Building ZINC001497046620 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046620' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046620 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001497046620 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046620/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046620 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/772 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1) `ZINC001497046620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001497046620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001497046620 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 24, 24, 24, 24, 24, 24, 27, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 24, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046620 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046620/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046620 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 773) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/773 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/773' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1) `ZINC001497046620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001497046620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001497046620 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 26, 26, 26, 26, 26, 26, 27, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 26, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046620 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001497046620 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046620/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046620/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046620 Building ZINC001497046620 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046620' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046620 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001497046620 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046620/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046620 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 772) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/772: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1) `ZINC001497046620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001497046620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001497046620 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 24, 24, 24, 24, 24, 24, 27, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 24, 24, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046620 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046620/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046620 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 773) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/773: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1) `ZINC001497046620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001497046620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001497046620 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 26, 26, 26, 26, 26, 26, 27, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 26, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046620 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001497046620 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046620/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046620/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046620 Building ZINC001497046623 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046623' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046623 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001497046623 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046623/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046623 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/774 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1) `ZINC001497046623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001497046623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001497046623 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 19, 32, 32, 32, 32, 32, 32, 35, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046623 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046623/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046623 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 775) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/775 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/775' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1) `ZINC001497046623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001497046623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001497046623 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 30, 30, 30, 30, 30, 30, 34, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 30, 30, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046623 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001497046623 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046623/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046623/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046623 Building ZINC001497046623 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046623' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046623 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001497046623 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046623/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046623 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 774) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/774: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1) `ZINC001497046623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001497046623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001497046623 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 19, 32, 32, 32, 32, 32, 32, 35, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 32, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046623 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046623/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046623 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 775) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/775: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1) `ZINC001497046623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001497046623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001497046623 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1C(=O)[C@H]1CC[C@@H](C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 30, 30, 30, 30, 30, 30, 34, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 30, 30, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046623 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001497046623 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046623/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046623/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497046623 Building ZINC001497345754 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497345754' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497345754 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001497345754 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497345754/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497345754 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/776 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001497345754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001497345754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497345754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001497345754 none CCCN(CCNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 12, 2, 2, 2, 5, 9, 12, 12, 20, 30, 30, 30, 30, 30, 30, 40, 40, 30, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 12, 12, 5, 5, 9, 9, 12, 30, 30, 30, 30, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 218 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497345754 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497345754/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497345754 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 777) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/777 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/777' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001497345754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001497345754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497345754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001497345754 none CCCN(CCNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 12, 2, 2, 2, 5, 10, 15, 15, 25, 31, 31, 31, 31, 31, 31, 36, 36, 31, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 12, 12, 5, 5, 10, 10, 15, 31, 31, 31, 31, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 203 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497345754 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001497345754 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497345754/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497345754/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497345754 Building ZINC001497345754 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497345754' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497345754 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001497345754 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497345754/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497345754 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 776) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/776: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001497345754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001497345754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497345754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001497345754 none CCCN(CCNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 12, 2, 2, 2, 5, 9, 12, 12, 20, 30, 30, 30, 30, 30, 30, 40, 40, 30, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 12, 12, 5, 5, 9, 9, 12, 30, 30, 30, 30, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 218 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497345754 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497345754/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497345754 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 777) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/777: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CCNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001497345754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001497345754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497345754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001497345754 none CCCN(CCNC(=O)[C@H]1CC[C@@H](C(N)=O)O1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 12, 2, 2, 2, 5, 10, 15, 15, 25, 31, 31, 31, 31, 31, 31, 36, 36, 31, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 12, 12, 5, 5, 10, 10, 15, 31, 31, 31, 31, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 203 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497345754 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001497345754 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497345754/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497345754/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001497345754 Building ZINC001498633788 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001498633788' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001498633788 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001498633788 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001498633788/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001498633788 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/778 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CNC(=O)CC[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001498633788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001498633788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001498633788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001498633788 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CNC(=O)CC[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 8, 16, 24, 24, 24, 39, 43, 49, 49, 49, 49, 49, 49, 50, 50, 49, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 16, 16, 24, 39, 39, 42, 42, 49, 49, 49, 49, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001498633788 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001498633788/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001498633788 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 779) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/779 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/779' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CNC(=O)CC[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001498633788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001498633788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001498633788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001498633788 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CNC(=O)CC[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 7, 12, 12, 12, 20, 26, 26, 26, 40, 43, 49, 49, 49, 49, 49, 49, 50, 50, 49, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 20, 20, 26, 40, 40, 42, 42, 49, 49, 49, 49, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 195 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001498633788 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001498633788 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001498633788/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001498633788/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001498633788 Building ZINC001498633788 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001498633788' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001498633788 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001498633788 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001498633788/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001498633788 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 778) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/778: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CNC(=O)CC[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001498633788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001498633788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001498633788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001498633788 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC(CNC(=O)CC[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 8, 8, 8, 16, 24, 24, 24, 39, 43, 49, 49, 49, 49, 49, 49, 50, 50, 49, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 16, 16, 24, 39, 39, 42, 42, 49, 49, 49, 49, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001498633788 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001498633788/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001498633788 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 779) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/779: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CNC(=O)CC[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001498633788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001498633788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001498633788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001498633788 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC(CNC(=O)CC[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 7, 12, 12, 12, 20, 26, 26, 26, 40, 43, 49, 49, 49, 49, 49, 49, 50, 50, 49, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 20, 20, 26, 40, 40, 42, 42, 49, 49, 49, 49, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 195 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001498633788 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001498633788 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001498633788/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001498633788/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001498633788 Building ZINC001506433332 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433332' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433332 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001506433332 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433332/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433332 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/780 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/780' -> `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@@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001506433332.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001506433332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001506433332 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 24, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 8, 8] 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]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433332 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433332/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433332 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 781) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/781 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/781' -> `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@@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001506433332.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001506433332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433332/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001506433332 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 21, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 8, 8] 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433332 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001506433332 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433332/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433332/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433332 Building ZINC001506433332 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433332' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433332 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001506433332 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433332/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433332 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 780) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/780: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001506433332.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001506433332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001506433332 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 24, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 8, 8] 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]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433332 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433332/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433332 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 781) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/781: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001506433332.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001506433332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433332/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001506433332 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 21, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 8, 8] 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433332 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001506433332 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433332/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433332/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433332 Building ZINC001506433333 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433333' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433333 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001506433333 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433333/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433333 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/782 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/782' -> `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@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001506433333.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001506433333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001506433333 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 9, 18, 28, 49, 49, 49, 49, 49, 49, 50, 50, 49, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 9, 49, 49, 49, 49, 50, 50, 9, 9] 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]) total number of confs: 136 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433333 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433333/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433333 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 783) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/783 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/783' -> `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@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001506433333.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001506433333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001506433333 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 7, 7, 7, 7, 18, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 7, 7] 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]) total number of confs: 136 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433333 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001506433333 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433333/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433333/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433333 Building ZINC001506433333 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433333' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433333 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001506433333 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433333/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433333 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 782) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/782: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001506433333.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001506433333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001506433333 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 9, 18, 28, 49, 49, 49, 49, 49, 49, 50, 50, 49, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 9, 49, 49, 49, 49, 50, 50, 9, 9] 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]) total number of confs: 136 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433333 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433333/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433333 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 783) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/783: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1) `ZINC001506433333.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001506433333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001506433333 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@]1(C)CCN(C(=O)[C@H]2CC[C@@H](C(N)=O)O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 7, 7, 7, 7, 18, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 7, 7] 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]) total number of confs: 136 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433333 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001506433333 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433333/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433333/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001506433333 Building ZINC001509144440 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001509144440' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001509144440 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001509144440 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001509144440/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001509144440 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/784 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)[C@H]2CC[C@@H](C(N)=O)C2)C1) `ZINC001509144440.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001509144440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001509144440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001509144440 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)[C@H]2CC[C@@H](C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 9, 14, 4, 4, 4, 15, 18, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 14, 14, 42, 4, 4, 44, 44, 44, 44, 44, 44, 44, 44, 4, 4] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 217 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001509144440 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001509144440/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001509144440 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 785) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/785 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/785' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)[C@H]2CC[C@@H](C(N)=O)C2)C1) `ZINC001509144440.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001509144440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001509144440/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001509144440 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)[C@H]2CC[C@@H](C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 8, 11, 7, 7, 7, 19, 20, 48, 48, 48, 48, 48, 48, 48, 48, 48, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 11, 11, 33, 7, 7, 48, 48, 48, 48, 48, 48, 48, 48, 7, 7] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 199 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001509144440 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001509144440 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001509144440/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001509144440/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001509144440 Building ZINC001509144440 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001509144440' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001509144440 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001509144440 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001509144440/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001509144440 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 784) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/784: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)[C@H]2CC[C@@H](C(N)=O)C2)C1) `ZINC001509144440.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001509144440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001509144440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001509144440 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)[C@H]2CC[C@@H](C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 9, 14, 4, 4, 4, 15, 18, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 14, 14, 42, 4, 4, 44, 44, 44, 44, 44, 44, 44, 44, 4, 4] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 217 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001509144440 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001509144440/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001509144440 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 785) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)[C@H]2CC[C@@H](C(N)=O)C2)C1) `ZINC001509144440.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001509144440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001509144440/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001509144440 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1(CCO)CN(C(=O)[C@H]2CC[C@@H](C(N)=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 8, 11, 7, 7, 7, 19, 20, 48, 48, 48, 48, 48, 48, 48, 48, 48, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 11, 11, 33, 7, 7, 48, 48, 48, 48, 48, 48, 48, 48, 7, 7] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 199 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001509144440 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001509144440 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001509144440/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001509144440/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001509144440 Building ZINC001512904203 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904203' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904203 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512904203 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904203/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904203 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/786 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3nn[nH]c3c2)C[C@H]1O) `ZINC001512904203.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512904203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001512904203 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3nn[nH]c3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 6, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 50, 50, 50, 14, 14, 42] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904203 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904203/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904203 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 787) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/787 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/787' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3nn[nH]c3c2)C[C@H]1O) `ZINC001512904203.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512904203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904203/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001512904203 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3nn[nH]c3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 6, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904203 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512904203 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904203/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904203/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904203 Building ZINC001512904203 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904203' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904203 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512904203 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904203/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904203 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 786) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/786: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3nn[nH]c3c2)C[C@H]1O) `ZINC001512904203.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512904203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001512904203 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3nn[nH]c3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 6, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 50, 50, 50, 14, 14, 42] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904203 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904203/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904203 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 787) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/787: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3nn[nH]c3c2)C[C@H]1O) `ZINC001512904203.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512904203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904203/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001512904203 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc3nn[nH]c3c2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 6, 1, 1, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904203 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512904203 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904203/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904203/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904203 Building ZINC001512904377 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904377' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904377 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512904377 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904377/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904377 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/788 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COC[C@@H]2CCOC2)C[C@H]1O) `ZINC001512904377.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512904377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001512904377 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COC[C@@H]2CCOC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 6, 6, 6, 6, 9, 9, 20, 28, 39, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 20, 20, 37, 37, 50, 50, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904377 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904377/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904377 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 789) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/789 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/789' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COC[C@@H]2CCOC2)C[C@H]1O) `ZINC001512904377.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512904377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904377/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001512904377 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COC[C@@H]2CCOC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 9, 9, 17, 25, 38, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 17, 17, 37, 37, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904377 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512904377 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904377/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904377/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904377 Building ZINC001512904377 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904377' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904377 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512904377 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904377/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904377 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 788) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/788: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COC[C@@H]2CCOC2)C[C@H]1O) `ZINC001512904377.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512904377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001512904377 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COC[C@@H]2CCOC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 6, 6, 6, 6, 9, 9, 20, 28, 39, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 20, 20, 37, 37, 50, 50, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904377 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904377/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904377 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 789) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/789: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COC[C@@H]2CCOC2)C[C@H]1O) `ZINC001512904377.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512904377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904377/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001512904377 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COC[C@@H]2CCOC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 9, 9, 17, 25, 38, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 17, 17, 37, 37, 50, 50, 50, 50, 50, 50, 7, 7, 21] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904377 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512904377 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904377/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904377/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904377 Building ZINC001512904380 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904380' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904380 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512904380 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904380/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904380 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/790 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COC[C@H]2CCOC2)C[C@H]1O) `ZINC001512904380.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512904380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001512904380 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COC[C@H]2CCOC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 10, 10, 21, 28, 39, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 21, 21, 37, 37, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904380 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904380/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904380 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 791) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/791 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/791' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COC[C@H]2CCOC2)C[C@H]1O) `ZINC001512904380.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512904380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001512904380 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COC[C@H]2CCOC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 8, 8, 16, 27, 40, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 16, 16, 38, 38, 50, 50, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904380 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512904380 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904380/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904380/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904380 Building ZINC001512904380 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904380' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904380 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512904380 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904380/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904380 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 790) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/790: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COC[C@H]2CCOC2)C[C@H]1O) `ZINC001512904380.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512904380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001512904380 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COC[C@H]2CCOC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 10, 10, 21, 28, 39, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 21, 21, 37, 37, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904380 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904380/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904380 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 791) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/791: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COC[C@H]2CCOC2)C[C@H]1O) `ZINC001512904380.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512904380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001512904380 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COC[C@H]2CCOC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 8, 8, 16, 27, 40, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 16, 16, 38, 38, 50, 50, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904380 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512904380 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904380/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904380/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904380 Building ZINC001512904469 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904469' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904469 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512904469 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904469/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904469 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/792 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nnc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001512904469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512904469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001512904469 none CCn1nnc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 42, 42, 42, 42, 42, 42, 23, 7, 23, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 42, 42, 42, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904469 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904469/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904469 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 793) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/793 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/793' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nnc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001512904469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512904469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001512904469 none CCn1nnc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 45, 45, 45, 45, 45, 26, 10, 26, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 45, 45, 45, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904469 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512904469 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904469/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904469/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904469 Building ZINC001512904469 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904469' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904469 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512904469 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904469/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904469 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 792) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/792: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nnc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001512904469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512904469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001512904469 none CCn1nnc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 42, 42, 42, 42, 42, 42, 23, 7, 23, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 42, 42, 42, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904469 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904469/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904469 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 793) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/793: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nnc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001512904469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512904469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001512904469 none CCn1nnc(C)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 45, 45, 45, 45, 45, 26, 10, 26, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 45, 45, 45, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904469 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512904469 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904469/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904469/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904469 Building ZINC001512904953 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904953' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904953 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512904953 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904953/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904953 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/794 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nc1) `ZINC001512904953.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512904953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001512904953 none COc1cnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 25, 25, 50, 50, 25, 12, 25, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904953 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904953/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904953 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 795) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/795 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/795' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nc1) `ZINC001512904953.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512904953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904953/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001512904953 none COc1cnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 44, 35, 50, 50, 25, 11, 25, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904953 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512904953 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904953/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904953/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904953 Building ZINC001512904953 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904953' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904953 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512904953 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904953/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904953 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 794) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/794: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nc1) `ZINC001512904953.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512904953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001512904953 none COc1cnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 25, 25, 50, 50, 25, 12, 25, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904953 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904953/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904953 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 795) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/795: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nc1) `ZINC001512904953.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512904953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904953/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001512904953 none COc1cnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.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, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 44, 35, 50, 50, 25, 11, 25, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50] 150 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904953 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512904953 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904953/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904953/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512904953 Building ZINC001512905160 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905160' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905160 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512905160 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905160/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905160 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/796 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3ncnn32)C[C@H]1O) `ZINC001512905160.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512905160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001512905160 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3ncnn32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 13, 13, 13, 13, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905160 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905160/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905160 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 797) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/797 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/797' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3ncnn32)C[C@H]1O) `ZINC001512905160.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512905160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001512905160 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3ncnn32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905160 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512905160 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905160/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905160/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905160 Building ZINC001512905160 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905160' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905160 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512905160 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905160/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905160 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 796) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/796: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3ncnn32)C[C@H]1O) `ZINC001512905160.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512905160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001512905160 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3ncnn32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 13, 13, 13, 13, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 50, 50, 50, 50, 13, 13, 39] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905160 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905160/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905160 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 797) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/797: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3ncnn32)C[C@H]1O) `ZINC001512905160.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512905160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001512905160 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2cccc3ncnn32)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905160 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512905160 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905160/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905160/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905160 Building ZINC001512905446 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905446' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905446 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512905446 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905446/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905446 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/798 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c(Cl)n1) `ZINC001512905446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512905446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001512905446 none Cn1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c(Cl)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 35, 11, 5, 11, 5, 5, 5, 5, 5, 3, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 35, 35, 5, 5, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 170 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905446 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905446/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905446 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 799) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/799 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/799' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c(Cl)n1) `ZINC001512905446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512905446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001512905446 none Cn1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c(Cl)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 29, 10, 7, 10, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 29, 29, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 157 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905446 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512905446 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905446/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905446/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905446 Building ZINC001512905446 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905446' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905446 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512905446 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905446/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905446 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 798) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/798: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c(Cl)n1) `ZINC001512905446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512905446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001512905446 none Cn1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c(Cl)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 35, 11, 5, 11, 5, 5, 5, 5, 5, 3, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 35, 35, 5, 5, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 170 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905446 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905446/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905446 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 799) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/799: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c(Cl)n1) `ZINC001512905446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512905446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001512905446 none Cn1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c(Cl)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 29, 10, 7, 10, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 29, 29, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 157 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905446 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512905446 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905446/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905446/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512905446 Building ZINC001512906133 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906133' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906133 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512906133 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906133/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906133 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/800 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCS(=O)(=O)CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001512906133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512906133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001512906133 none CCCS(=O)(=O)CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 48, 40, 48, 48, 13, 6, 13, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 40, 40, 6, 6, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906133 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906133/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906133 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 801) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/801 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/801' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCS(=O)(=O)CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001512906133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512906133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001512906133 none CCCS(=O)(=O)CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 49, 40, 49, 49, 12, 6, 12, 6, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 40, 40, 6, 6, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906133 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512906133 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906133/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906133/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906133 Building ZINC001512906133 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906133' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906133 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512906133 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906133/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906133 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 800) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/800: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCS(=O)(=O)CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001512906133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512906133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001512906133 none CCCS(=O)(=O)CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 48, 40, 48, 48, 13, 6, 13, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 40, 40, 6, 6, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906133 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906133/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906133 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 801) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/801: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCS(=O)(=O)CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001512906133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512906133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001512906133 none CCCS(=O)(=O)CC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 49, 40, 49, 49, 12, 6, 12, 6, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 40, 40, 6, 6, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906133 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512906133 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906133/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906133/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906133 Building ZINC001512906383 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906383' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906383 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512906383 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906383/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906383 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/802 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nc1) `ZINC001512906383.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512906383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001512906383 none COc1ccc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 38, 12, 7, 12, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 38, 38, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906383 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906383/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906383 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 803) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/803 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/803' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nc1) `ZINC001512906383.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512906383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906383/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001512906383 none COc1ccc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 37, 9, 5, 9, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 37, 37, 5, 5, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49, 50]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906383 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512906383 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906383/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906383/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906383 Building ZINC001512906383 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906383' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906383 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512906383 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906383/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906383 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 802) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/802: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nc1) `ZINC001512906383.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512906383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001512906383 none COc1ccc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 38, 12, 7, 12, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 38, 38, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 50] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906383 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906383/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906383 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 803) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/803: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nc1) `ZINC001512906383.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512906383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906383/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001512906383 none COc1ccc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 37, 9, 5, 9, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 37, 37, 5, 5, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49, 50]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906383 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512906383 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906383/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906383/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906383 Building ZINC001512906542 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906542' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906542 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512906542 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906542/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906542 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/804 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001512906542.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512906542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001512906542 none CCn1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 29, 29, 29, 20, 7, 4, 7, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 29, 29, 50, 50, 50, 50, 50, 29, 20, 20, 4, 4, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 29] 150 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49, 50]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906542 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906542/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906542 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 805) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/805 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/805' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001512906542.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512906542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906542/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001512906542 none CCn1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 29, 29, 29, 21, 7, 4, 7, 4, 4, 4, 4, 4, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 29, 29, 50, 50, 50, 50, 50, 29, 21, 21, 4, 4, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 29] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49, 50]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906542 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512906542 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906542/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906542/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906542 Building ZINC001512906542 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906542' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906542 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512906542 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906542/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906542 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 804) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/804: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001512906542.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512906542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001512906542 none CCn1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 29, 29, 29, 20, 7, 4, 7, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 29, 29, 50, 50, 50, 50, 50, 29, 20, 20, 4, 4, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 29] 150 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49, 50]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906542 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906542/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906542 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 805) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/805: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001512906542.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512906542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906542/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001512906542 none CCn1cc(CC(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 29, 29, 29, 21, 7, 4, 7, 4, 4, 4, 4, 4, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 29, 29, 50, 50, 50, 50, 50, 29, 21, 21, 4, 4, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 29] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49, 50]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906542 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512906542 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906542/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906542/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512906542 Building ZINC001512907400 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907400' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512907400 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907400/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/806 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1[C@@H]1C[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001512907400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512907400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001512907400 none Cn1nccc1[C@@H]1C[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 34, 34, 34, 34, 17, 34, 10, 17, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 34, 34, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907400/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 807) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/807 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/807' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1[C@@H]1C[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001512907400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512907400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001512907400 none Cn1nccc1[C@@H]1C[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 32, 32, 32, 32, 14, 32, 7, 14, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 32, 32, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512907400 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907400/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907400/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907400 Building ZINC001512907400 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907400' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512907400 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907400/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 806) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/806: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1[C@@H]1C[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001512907400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512907400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001512907400 none Cn1nccc1[C@@H]1C[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 34, 34, 34, 34, 17, 34, 10, 17, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 34, 34, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907400/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 807) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/807: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1[C@@H]1C[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001512907400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512907400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001512907400 none Cn1nccc1[C@@H]1C[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 32, 32, 32, 32, 14, 32, 7, 14, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 32, 32, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907400 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512907400 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907400/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907400/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907400 Building ZINC001512907430 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907430' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907430 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512907430 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907430/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907430 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/808 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001512907430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512907430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001512907430 none CCCn1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.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, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 33, 33, 12, 7, 12, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907430 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907430/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907430 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 809) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/809 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/809' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001512907430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512907430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001512907430 none CCCn1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.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, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 32, 32, 32, 14, 7, 14, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907430 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512907430 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907430/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907430/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907430 Building ZINC001512907430 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907430' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907430 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512907430 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907430/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907430 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 808) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/808: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001512907430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512907430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001512907430 none CCCn1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.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, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 33, 33, 12, 7, 12, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907430 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907430/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907430 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 809) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/809: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001512907430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512907430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001512907430 none CCCn1cc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.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, 8, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 32, 32, 32, 14, 7, 14, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907430 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512907430 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907430/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907430/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907430 Building ZINC001512907435 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907435' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907435 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512907435 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907435/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907435 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/810 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c[nH]c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cc1=O) `ZINC001512907435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512907435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001512907435 none COc1c[nH]c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 6, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 24, 10, 24, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907435 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907435/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907435 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 811) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/811 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/811' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c[nH]c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cc1=O) `ZINC001512907435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512907435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001512907435 none COc1c[nH]c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 6, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 22, 9, 22, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/323031/xbw-8058115.49/working/building/ZINC001512907435 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512907435 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907435/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907435/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907435 Building ZINC001512907435 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907435' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907435 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512907435 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907435/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907435 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 810) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/810: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c[nH]c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cc1=O) `ZINC001512907435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512907435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001512907435 none COc1c[nH]c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 6, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 24, 10, 24, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907435 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907435/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907435 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 811) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/811: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c[nH]c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cc1=O) `ZINC001512907435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512907435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001512907435 none COc1c[nH]c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 6, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 22, 9, 22, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/323031/xbw-8058115.49/working/building/ZINC001512907435 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512907435 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907435/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907435/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907435 Building ZINC001512907466 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907466' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907466 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512907466 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907466/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907466 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/812 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cnn1C) `ZINC001512907466.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512907466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001512907466 none COc1c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 12, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 27, 11, 27, 11, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 143 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907466 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907466/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907466 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 813) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/813 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/813' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cnn1C) `ZINC001512907466.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512907466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907466/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001512907466 none COc1c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 12, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 26, 10, 26, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907466 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512907466 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907466/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907466/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907466 Building ZINC001512907466 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907466' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907466 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512907466 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907466/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907466 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 812) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/812: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cnn1C) `ZINC001512907466.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512907466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001512907466 none COc1c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 12, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 27, 11, 27, 11, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 143 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907466 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907466/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907466 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 813) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/813: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cnn1C) `ZINC001512907466.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512907466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907466/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001512907466 none COc1c(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 12, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 26, 10, 26, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907466 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512907466 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907466/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907466/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512907466 Building ZINC001512908204 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908204' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908204 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512908204 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908204/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908204 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/814 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CNC(=O)C2CCCC2)C[C@H]1O) `ZINC001512908204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512908204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001512908204 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CNC(=O)C2CCCC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 10, 10, 21, 32, 32, 32, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 21, 21, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908204 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908204/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908204 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 815) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/815 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/815' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CNC(=O)C2CCCC2)C[C@H]1O) `ZINC001512908204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512908204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001512908204 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CNC(=O)C2CCCC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 20, 31, 31, 31, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 20, 20, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908204 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512908204 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908204/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908204/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908204 Building ZINC001512908204 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908204' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908204 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512908204 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908204/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908204 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 814) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/814: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CNC(=O)C2CCCC2)C[C@H]1O) `ZINC001512908204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512908204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001512908204 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CNC(=O)C2CCCC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 10, 10, 21, 32, 32, 32, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 21, 21, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908204 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908204/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908204 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 815) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/815: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CNC(=O)C2CCCC2)C[C@H]1O) `ZINC001512908204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512908204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001512908204 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CNC(=O)C2CCCC2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 4, 7, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 20, 31, 31, 31, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 20, 20, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908204 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512908204 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908204/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908204/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908204 Building ZINC001512908801 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908801' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908801 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512908801 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908801/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908801 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/816 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001512908801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512908801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001512908801 none CC(C)NC(=O)CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 35, 50, 25, 23, 9, 6, 9, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 34, 33, 28, 28, 23, 23, 6, 6, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908801 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908801/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908801 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 817) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/817 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/817' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001512908801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512908801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001512908801 none CC(C)NC(=O)CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 31, 50, 24, 23, 10, 7, 10, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 26, 26, 23, 23, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908801 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512908801 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908801/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908801/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908801 Building ZINC001512908801 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908801' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908801 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512908801 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908801/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908801 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 816) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/816: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001512908801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512908801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001512908801 none CC(C)NC(=O)CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 35, 50, 25, 23, 9, 6, 9, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 50, 34, 33, 28, 28, 23, 23, 6, 6, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908801 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908801/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908801 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 817) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/817: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001512908801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512908801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001512908801 none CC(C)NC(=O)CCCC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 31, 50, 24, 23, 10, 7, 10, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 26, 26, 23, 23, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 150 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 55, 56]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908801 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512908801 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908801/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908801/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908801 Building ZINC001512908822 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908822' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908822 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512908822 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908822/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908822 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/818 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3n[nH]cc3C2)C[C@H]1O) `ZINC001512908822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512908822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001512908822 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3n[nH]cc3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 26, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 174 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908822 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908822/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908822 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 819) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/819 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/819' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3n[nH]cc3C2)C[C@H]1O) `ZINC001512908822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512908822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001512908822 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3n[nH]cc3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 26, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 163 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908822 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512908822 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908822/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908822/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908822 Building ZINC001512908822 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908822' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908822 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512908822 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908822/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908822 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 818) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/818: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3n[nH]cc3C2)C[C@H]1O) `ZINC001512908822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512908822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001512908822 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3n[nH]cc3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 26, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 174 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908822 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908822/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908822 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 819) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/819: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3n[nH]cc3C2)C[C@H]1O) `ZINC001512908822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512908822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001512908822 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3n[nH]cc3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 26, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 163 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908822 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512908822 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908822/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908822/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908822 Building ZINC001512908823 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908823' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908823 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512908823 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908823/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908823 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/820 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3n[nH]cc3C2)C[C@H]1O) `ZINC001512908823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512908823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001512908823 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3n[nH]cc3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 23, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 171 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908823 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908823/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908823 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 821) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/821 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/821' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3n[nH]cc3C2)C[C@H]1O) `ZINC001512908823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512908823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001512908823 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3n[nH]cc3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 23, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 167 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908823 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512908823 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908823/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908823/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908823 Building ZINC001512908823 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908823' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908823 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512908823 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908823/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908823 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 820) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/820: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3n[nH]cc3C2)C[C@H]1O) `ZINC001512908823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512908823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001512908823 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3n[nH]cc3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 23, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 171 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908823 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908823/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908823 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 821) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/821: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3n[nH]cc3C2)C[C@H]1O) `ZINC001512908823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512908823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001512908823 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3n[nH]cc3C2)C[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 23, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 167 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908823 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512908823 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908823/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908823/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512908823 Building ZINC001512909301 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909301' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909301 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512909301 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909301/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909301 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/822 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(Cl)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001512909301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512909301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001512909301 none Cn1ncc(Cl)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 12, 34, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909301 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909301/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909301 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 823) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/823 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/823' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(Cl)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001512909301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512909301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001512909301 none Cn1ncc(Cl)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 30, 11, 30, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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/323031/xbw-8058115.49/working/building/ZINC001512909301 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512909301 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909301/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909301/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909301 Building ZINC001512909301 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909301' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909301 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512909301 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909301/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909301 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 822) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/822: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(Cl)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001512909301.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512909301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001512909301 none Cn1ncc(Cl)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 12, 34, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909301 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909301/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909301 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 823) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/823: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(Cl)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001512909301.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512909301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001512909301 none Cn1ncc(Cl)c1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 30, 11, 30, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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/323031/xbw-8058115.49/working/building/ZINC001512909301 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512909301 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909301/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909301/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909301 Building ZINC001512909384 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909384' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909384 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512909384 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909384/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909384 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/824 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001512909384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512909384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001512909384 none CCN1C[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 33, 33, 33, 13, 33, 7, 13, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 33, 33, 33, 50, 50, 50, 50, 50, 33, 33, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 33, 33] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 218 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909384 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909384/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909384 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 825) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/825 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/825' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001512909384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512909384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001512909384 none CCN1C[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 28, 28, 28, 12, 28, 8, 12, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 28, 28, 28, 50, 50, 50, 50, 50, 28, 28, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 28, 28] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 235 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909384 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512909384 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909384/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909384/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909384 Building ZINC001512909384 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909384' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909384 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512909384 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909384/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909384 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 824) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/824: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001512909384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512909384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001512909384 none CCN1C[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 33, 33, 33, 13, 33, 7, 13, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 33, 33, 33, 50, 50, 50, 50, 50, 33, 33, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 33, 33] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 218 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909384 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909384/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909384 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 825) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/825: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001512909384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512909384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001512909384 none CCN1C[C@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 28, 28, 28, 12, 28, 8, 12, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 28, 28, 28, 50, 50, 50, 50, 50, 28, 28, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 28, 28] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 235 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909384 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512909384 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909384/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909384/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909384 Building ZINC001512909388 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909388' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909388 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512909388 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909388/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909388 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/826 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001512909388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512909388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001512909388 none CCN1C[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 30, 30, 30, 11, 30, 7, 11, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 30, 30, 30, 50, 50, 50, 50, 50, 30, 30, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 30, 30] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909388 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909388/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909388 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 827) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/827 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/827' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001512909388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512909388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001512909388 none CCN1C[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 28, 28, 28, 11, 28, 6, 11, 6, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 28, 28, 28, 50, 50, 50, 50, 50, 28, 28, 6, 6, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 28, 28] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 231 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909388 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512909388 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909388/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909388/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909388 Building ZINC001512909388 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909388' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909388 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512909388 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909388/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909388 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 826) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/826: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001512909388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512909388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001512909388 none CCN1C[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 30, 30, 30, 11, 30, 7, 11, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 30, 30, 30, 50, 50, 50, 50, 50, 30, 30, 7, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 30, 30] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909388 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909388/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909388 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 827) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/827: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O) `ZINC001512909388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512909388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001512909388 none CCN1C[C@@H](C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 28, 28, 28, 11, 28, 6, 11, 6, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 28, 28, 28, 50, 50, 50, 50, 50, 28, 28, 6, 6, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 28, 28] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 231 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909388 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512909388 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909388/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909388/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909388 Building ZINC001512909872 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909872' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909872 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512909872 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909872/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909872 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/828 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001512909872.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512909872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001512909872 none CC(=O)N1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 44, 50, 44, 44, 44, 44, 31, 44, 12, 31, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 44, 44, 44, 44, 44, 44, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 197 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909872 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909872/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909872 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 829) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/829 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/829' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001512909872.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512909872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909872/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001512909872 none CC(=O)N1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 42, 50, 42, 42, 42, 42, 31, 42, 13, 31, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 42, 42, 42, 42, 42, 42, 13, 13, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 200 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909872 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512909872 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909872/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909872/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909872 Building ZINC001512909872 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909872' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909872 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512909872 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909872/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909872 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 828) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/828: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001512909872.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512909872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001512909872 none CC(=O)N1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 44, 50, 44, 44, 44, 44, 31, 44, 12, 31, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 44, 44, 44, 44, 44, 44, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 197 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909872 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909872/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909872 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 829) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/829: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001512909872.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512909872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909872/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001512909872 none CC(=O)N1CCC[C@H]1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 42, 50, 42, 42, 42, 42, 31, 42, 13, 31, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 42, 42, 42, 42, 42, 42, 13, 13, 39, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 200 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909872 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512909872 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909872/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909872/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909872 Building ZINC001512909937 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909937' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909937 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512909937 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909937/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909937 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/830 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nn(C)cc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001512909937.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512909937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001512909937 none COc1nn(C)cc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 26, 10, 26, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 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, 47, 48]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909937 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909937/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909937 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 831) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/831 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/831' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nn(C)cc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001512909937.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512909937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909937/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001512909937 none COc1nn(C)cc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 22, 9, 22, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 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, 47, 48]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909937 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512909937 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909937/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909937/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909937 Building ZINC001512909937 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909937' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909937 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512909937 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909937/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909937 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 830) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/830: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nn(C)cc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001512909937.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512909937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001512909937 none COc1nn(C)cc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 26, 10, 26, 10, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 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, 47, 48]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909937 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909937/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909937 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 831) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/831: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nn(C)cc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001512909937.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512909937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909937/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001512909937 none COc1nn(C)cc1C(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 22, 9, 22, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 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, 47, 48]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909937 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512909937 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909937/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909937/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512909937 Building ZINC001512910493 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512910493' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512910493 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512910493 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512910493/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512910493 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/832 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1nnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001512910493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512910493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512910493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001512910493 none CC(C)(C)n1nnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 22, 12, 22, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512910493 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512910493/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512910493 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 833) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/833 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/833' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1nnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001512910493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512910493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512910493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001512910493 none CC(C)(C)n1nnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 17, 8, 17, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512910493 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512910493 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512910493/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512910493/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512910493 Building ZINC001512910493 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512910493' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512910493 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512910493 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512910493/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512910493 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 832) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/832: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1nnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001512910493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512910493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512910493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001512910493 none CC(C)(C)n1nnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 22, 12, 22, 12, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512910493 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512910493/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512910493 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 833) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/833: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1nnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001512910493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512910493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512910493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001512910493 none CC(C)(C)n1nnc(C(=O)N2C[C@@H](O)[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 17, 8, 17, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 24, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 150 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512910493 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512910493 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512910493/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512910493/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512910493 Building ZINC001512952687 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512952687' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512952687 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512952687 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512952687/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512952687 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/834 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCN2CCCC2=O)C1) `ZINC001512952687.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512952687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512952687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001512952687 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCN2CCCC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 8, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 41, 46, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 12, 41, 41, 46, 46, 50, 50, 50, 50, 50, 50, 5, 5] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512952687 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512952687/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512952687 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 835) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/835 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/835' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCN2CCCC2=O)C1) `ZINC001512952687.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512952687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512952687/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001512952687 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCN2CCCC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 8, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 7, 10, 10, 10, 10, 10, 10, 10, 16, 16, 16, 43, 46, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 30, 16, 43, 43, 46, 46, 50, 50, 50, 50, 50, 50, 10, 10] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512952687 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512952687 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512952687/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512952687/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512952687 Building ZINC001512952687 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512952687' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512952687 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512952687 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512952687/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512952687 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 834) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/834: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCN2CCCC2=O)C1) `ZINC001512952687.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512952687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512952687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001512952687 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCN2CCCC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 8, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 41, 46, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 12, 41, 41, 46, 46, 50, 50, 50, 50, 50, 50, 5, 5] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512952687 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512952687/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512952687 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 835) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/835: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCN2CCCC2=O)C1) `ZINC001512952687.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512952687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512952687/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001512952687 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)CCN2CCCC2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 8, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 7, 10, 10, 10, 10, 10, 10, 10, 16, 16, 16, 43, 46, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 30, 16, 43, 43, 46, 46, 50, 50, 50, 50, 50, 50, 10, 10] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512952687 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512952687 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512952687/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512952687/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512952687 Building ZINC001512956102 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956102' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512956102 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956102/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/836 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1=O) `ZINC001512956102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512956102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001512956102 none CC[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 45, 16, 45, 16, 16, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 45, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956102/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 837) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/837 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/837' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1=O) `ZINC001512956102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512956102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001512956102 none CC[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [47, 44, 17, 44, 17, 17, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 44, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 17, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512956102 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956102/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956102/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956102 Building ZINC001512956102 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956102' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512956102 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956102/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 836) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/836: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1=O) `ZINC001512956102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512956102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001512956102 none CC[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 45, 16, 45, 16, 16, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 45, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956102/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 837) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/837: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1=O) `ZINC001512956102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512956102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001512956102 none CC[C@@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [47, 44, 17, 44, 17, 17, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 44, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 17, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956102 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512956102 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956102/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956102/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956102 Building ZINC001512956104 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956104' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956104 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512956104 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956104/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956104 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/838 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1=O) `ZINC001512956104.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512956104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001512956104 none CC[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 45, 24, 45, 24, 24, 10, 10, 10, 10, 4, 1, 9, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 45, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 24, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 30, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956104 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956104/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956104 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 839) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/839 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/839' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1=O) `ZINC001512956104.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512956104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956104/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001512956104 none CC[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 42, 17, 42, 17, 17, 7, 7, 7, 7, 4, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 42, 50, 50, 50, 50, 50, 45, 45, 45, 45, 45, 17, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956104 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512956104 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956104/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956104/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956104 Building ZINC001512956104 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956104' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956104 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512956104 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956104/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956104 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 838) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/838: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1=O) `ZINC001512956104.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512956104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001512956104 none CC[C@H](C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 45, 24, 45, 24, 24, 10, 10, 10, 10, 4, 1, 9, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 45, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 24, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 30, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956104 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956104/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956104 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 839) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/839: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1=O) `ZINC001512956104.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512956104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956104/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001512956104 none CC[C@H](C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1O)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 42, 17, 42, 17, 17, 7, 7, 7, 7, 4, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 42, 50, 50, 50, 50, 50, 45, 45, 45, 45, 45, 17, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956104 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512956104 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956104/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956104/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512956104 Building ZINC001512979429 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512979429' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512979429 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512979429 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512979429/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512979429 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/840 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CCOCC1) `ZINC001512979429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512979429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512979429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001512979429 none COCC1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 19, 18, 18, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 18, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 33, 33, 33, 33, 33, 33, 33, 33] 150 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512979429 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512979429/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512979429 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 841) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/841 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/841' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CCOCC1) `ZINC001512979429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512979429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512979429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001512979429 none COCC1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 41, 24, 23, 23, 8, 8, 8, 8, 5, 1, 7, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 41, 41, 41, 41, 41, 50, 50, 50, 50, 50, 23, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 24, 41, 41, 41, 41, 41, 41, 41, 41] 150 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512979429 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512979429 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512979429/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512979429/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512979429 Building ZINC001512979429 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512979429' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512979429 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512979429 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512979429/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512979429 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 840) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/840: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CCOCC1) `ZINC001512979429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512979429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512979429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001512979429 none COCC1(C(=O)N[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 33, 19, 18, 18, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 18, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 33, 33, 33, 33, 33, 33, 33, 33] 150 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512979429 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512979429/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512979429 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 841) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/841: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CCOCC1) `ZINC001512979429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512979429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512979429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001512979429 none COCC1(C(=O)N[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2O)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 41, 24, 23, 23, 8, 8, 8, 8, 5, 1, 7, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 41, 41, 41, 41, 41, 50, 50, 50, 50, 50, 23, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 24, 41, 41, 41, 41, 41, 41, 41, 41] 150 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512979429 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512979429 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512979429/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512979429/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512979429 Building ZINC001512992573 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512992573' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512992573 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512992573 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512992573/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512992573 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/842 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)C(=O)Nc2ccccc2)C1) `ZINC001512992573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512992573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512992573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001512992573 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)C(=O)Nc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 6, 7, 7, 7, 7, 7, 7, 7, 21, 21, 21, 45, 45, 45, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21, 21, 45, 50, 50, 50, 50, 50, 7, 7] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512992573 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512992573/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512992573 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 843) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/843 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/843' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)C(=O)Nc2ccccc2)C1) `ZINC001512992573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512992573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512992573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001512992573 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)C(=O)Nc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 7, 10, 10, 10, 10, 10, 10, 10, 29, 29, 29, 46, 45, 45, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 30, 29, 46, 50, 50, 50, 50, 50, 10, 10] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512992573 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512992573 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512992573/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512992573/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512992573 Building ZINC001512992573 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512992573' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512992573 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001512992573 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512992573/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512992573 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 842) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/842: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)C(=O)Nc2ccccc2)C1) `ZINC001512992573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001512992573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512992573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001512992573 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)C(=O)Nc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 6, 7, 7, 7, 7, 7, 7, 7, 21, 21, 21, 45, 45, 45, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21, 21, 45, 50, 50, 50, 50, 50, 7, 7] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512992573 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512992573/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512992573 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 843) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/843: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)C(=O)Nc2ccccc2)C1) `ZINC001512992573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001512992573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512992573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001512992573 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](O)[C@H](NC(=O)C(=O)Nc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 7, 10, 10, 10, 10, 10, 10, 10, 29, 29, 29, 46, 45, 45, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 30, 29, 46, 50, 50, 50, 50, 50, 10, 10] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512992573 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001512992573 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512992573/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512992573/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001512992573 Building ZINC001513220445 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513220445' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513220445 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513220445 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513220445/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513220445 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/844 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCNS(C)(=O)=O) `ZINC001513220445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513220445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513220445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001513220445 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 4, 4, 20, 21, 42, 50, 50, 50, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 20, 20, 21, 21, 42, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513220445 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513220445/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513220445 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 845) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/845 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/845' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCNS(C)(=O)=O) `ZINC001513220445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513220445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513220445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001513220445 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 5, 5, 21, 23, 42, 50, 50, 50, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 21, 21, 23, 23, 42, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513220445 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513220445 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513220445/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513220445/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513220445 Building ZINC001513220445 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513220445' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513220445 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513220445 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513220445/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513220445 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 844) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/844: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCNS(C)(=O)=O) `ZINC001513220445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513220445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513220445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001513220445 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 4, 4, 20, 21, 42, 50, 50, 50, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 20, 20, 21, 21, 42, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513220445 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513220445/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513220445 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 845) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/845: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCNS(C)(=O)=O) `ZINC001513220445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513220445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513220445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001513220445 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)CCNS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 5, 5, 21, 23, 42, 50, 50, 50, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 21, 21, 23, 23, 42, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513220445 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513220445 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513220445/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513220445/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513220445 Building ZINC001513350139 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350139' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350139 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513350139 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350139/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350139 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/846 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001513350139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513350139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350139 none CCNC(=O)CCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 30, 34, 27, 12, 8, 12, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 9, 8, 50, 50, 50, 50, 50, 34, 30, 30, 27, 27, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 8, 8] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350139 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350139/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350139 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 847) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/847 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/847' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001513350139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513350139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350139 none CCNC(=O)CCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 31, 32, 29, 10, 7, 10, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 9, 7, 50, 50, 50, 50, 50, 32, 31, 31, 29, 29, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 7, 7] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350139 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513350139 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350139/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350139/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350139 Building ZINC001513350139 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350139' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350139 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513350139 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350139/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350139 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 846) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/846: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001513350139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513350139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350139 none CCNC(=O)CCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 30, 34, 27, 12, 8, 12, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 9, 8, 50, 50, 50, 50, 50, 34, 30, 30, 27, 27, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 8, 8] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350139 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350139/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350139 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 847) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/847: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001513350139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513350139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350139 none CCNC(=O)CCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 31, 32, 29, 10, 7, 10, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 9, 7, 50, 50, 50, 50, 50, 32, 31, 31, 29, 29, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 7, 7] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52, 53]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350139 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513350139 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350139/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350139/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350139 Building ZINC001513350880 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001513350880 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/848 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001513350880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513350880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350880 none CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [19, 14, 14, 14, 14, 14, 14, 31, 32, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 849) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/849 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/849' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001513350880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513350880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350880 none CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [21, 14, 14, 14, 14, 14, 14, 30, 32, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 168 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 850) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/850 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/850' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001513350880.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001513350880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350880 none CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [19, 14, 14, 14, 14, 14, 14, 31, 32, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 851) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/851 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/851' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001513350880.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001513350880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350880 none CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [21, 14, 14, 14, 14, 14, 14, 30, 32, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 168 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513350880 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 Building ZINC001513350880 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001513350880 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 848) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/848: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001513350880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513350880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350880 none CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [19, 14, 14, 14, 14, 14, 14, 31, 32, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 849) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/849: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001513350880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513350880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350880 none CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [21, 14, 14, 14, 14, 14, 14, 30, 32, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 168 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 850) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/850: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001513350880.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001513350880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350880 none CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [19, 14, 14, 14, 14, 14, 14, 31, 32, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 851) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/851: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001513350880.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001513350880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350880 none CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [21, 14, 14, 14, 14, 14, 14, 30, 32, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 168 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513350880 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 Building ZINC001513350880 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001513350880 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 848) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/848: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001513350880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513350880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350880 none CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [19, 14, 14, 14, 14, 14, 14, 31, 32, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 849) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/849: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001513350880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513350880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350880 none CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [21, 14, 14, 14, 14, 14, 14, 30, 32, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 168 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 850) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/850: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001513350880.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001513350880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350880 none CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [19, 14, 14, 14, 14, 14, 14, 31, 32, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 851) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/851: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001513350880.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001513350880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350880 none CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [21, 14, 14, 14, 14, 14, 14, 30, 32, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 168 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513350880 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 Building ZINC001513350880 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001513350880 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 848) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/848: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001513350880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513350880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350880 none CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [19, 14, 14, 14, 14, 14, 14, 31, 32, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 849) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/849: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001513350880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513350880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350880 none CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [21, 14, 14, 14, 14, 14, 14, 30, 32, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 168 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 850) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/850: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001513350880.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001513350880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350880 none CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [19, 14, 14, 14, 14, 14, 14, 31, 32, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 19, 19, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 851) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/851: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001513350880.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001513350880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350880 none CO[C@@H]1CN(C(=O)[C@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [21, 14, 14, 14, 14, 14, 14, 30, 32, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 168 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513350880 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350880 Building ZINC001513350882 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001513350882 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/852 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001513350882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513350882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350882 none CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [18, 13, 13, 13, 13, 13, 13, 32, 34, 50, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 158 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 853) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/853 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/853' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001513350882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513350882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350882 none CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [17, 14, 14, 14, 14, 14, 14, 34, 37, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 854) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/854 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/854' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001513350882.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001513350882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350882 none CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [18, 13, 13, 13, 13, 13, 13, 32, 34, 50, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 158 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 855) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/855 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/855' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001513350882.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001513350882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350882 none CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [17, 14, 14, 14, 14, 14, 14, 34, 37, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513350882 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 Building ZINC001513350882 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001513350882 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 852) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/852: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001513350882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513350882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350882 none CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [18, 13, 13, 13, 13, 13, 13, 32, 34, 50, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 158 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 853) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/853: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001513350882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513350882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350882 none CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [17, 14, 14, 14, 14, 14, 14, 34, 37, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 854) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/854: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001513350882.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001513350882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350882 none CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [18, 13, 13, 13, 13, 13, 13, 32, 34, 50, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 158 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 855) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/855: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001513350882.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001513350882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350882 none CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [17, 14, 14, 14, 14, 14, 14, 34, 37, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513350882 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 Building ZINC001513350882 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001513350882 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 852) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/852: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001513350882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513350882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350882 none CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [18, 13, 13, 13, 13, 13, 13, 32, 34, 50, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 158 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 853) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/853: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001513350882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513350882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350882 none CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [17, 14, 14, 14, 14, 14, 14, 34, 37, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 854) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/854: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001513350882.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001513350882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350882 none CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [18, 13, 13, 13, 13, 13, 13, 32, 34, 50, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 158 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 855) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/855: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001513350882.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001513350882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350882 none CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [17, 14, 14, 14, 14, 14, 14, 34, 37, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513350882 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 Building ZINC001513350882 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001513350882 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 852) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/852: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001513350882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513350882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350882 none CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [18, 13, 13, 13, 13, 13, 13, 32, 34, 50, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 158 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 853) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/853: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001513350882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513350882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350882 none CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [17, 14, 14, 14, 14, 14, 14, 34, 37, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `2' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/2 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 2 (index: 854) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/854: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001513350882.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001513350882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350882 none CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [18, 13, 13, 13, 13, 13, 13, 32, 34, 50, 50, 50, 50, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 158 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `3' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/3 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 3 (index: 855) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/855: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001513350882.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001513350882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513350882 none CO[C@@H]1CN(C(=O)[C@@H]2CN(C)CCO2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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: [17, 14, 14, 14, 14, 14, 14, 34, 37, 50, 50, 50, 50, 50, 50, 50, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 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/323031/xbw-8058115.49/working/building/ZINC001513350882 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513350882 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 2: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/2.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/0.* 3: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882/3.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350882 Building ZINC001513350896 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350896' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350896 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513350896 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350896/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350896 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/856 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001513350896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513350896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001513350896 none CCn1nncc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 36, 36, 36, 36, 19, 8, 19, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 12, 8, 50, 50, 50, 50, 50, 36, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 8, 8] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350896 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350896/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350896 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 857) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/857 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/857' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001513350896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513350896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001513350896 none CCn1nncc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 36, 36, 36, 36, 22, 10, 22, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 14, 10, 50, 50, 50, 50, 50, 36, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 10, 10] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350896 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513350896 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350896/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350896/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350896 Building ZINC001513350896 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350896' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350896 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513350896 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350896/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350896 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 856) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/856: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001513350896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513350896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001513350896 none CCn1nncc1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 36, 36, 36, 36, 19, 8, 19, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 12, 8, 50, 50, 50, 50, 50, 36, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 8, 8] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350896 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350896/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350896 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 857) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/857: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1) `ZINC001513350896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513350896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001513350896 none CCn1nncc1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 36, 36, 36, 36, 22, 10, 22, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 14, 10, 50, 50, 50, 50, 50, 36, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 10, 10] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350896 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513350896 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350896/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350896/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513350896 Building ZINC001513351280 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351280' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351280 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513351280 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351280/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351280 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/858 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2cn(C)c(=O)cn2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001513351280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513351280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001513351280 none CO[C@@H]1CN(C(=O)c2cn(C)c(=O)cn2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 8, 5, 1, 11, 1, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 12, 12, 28, 28, 50, 50, 50, 50, 50, 50, 50, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 12, 12, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351280 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351280/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351280 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 859) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/859 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/859' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2cn(C)c(=O)cn2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001513351280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513351280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001513351280 none CO[C@@H]1CN(C(=O)c2cn(C)c(=O)cn2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 8, 5, 1, 11, 1, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 50, 50, 50, 50, 50, 50, 50, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351280 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513351280 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351280/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351280/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351280 Building ZINC001513351280 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351280' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351280 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513351280 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351280/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351280 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 858) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/858: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2cn(C)c(=O)cn2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001513351280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513351280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001513351280 none CO[C@@H]1CN(C(=O)c2cn(C)c(=O)cn2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 8, 5, 1, 11, 1, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 12, 12, 28, 28, 50, 50, 50, 50, 50, 50, 50, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 12, 12, 50, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351280 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351280/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351280 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 859) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/859: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)c2cn(C)c(=O)cn2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001513351280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513351280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001513351280 none CO[C@@H]1CN(C(=O)c2cn(C)c(=O)cn2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 8, 5, 1, 11, 1, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 50, 50, 50, 50, 50, 50, 50, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351280 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513351280 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351280/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351280/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351280 Building ZINC001513351632 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351632' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351632 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513351632 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351632/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351632 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/860 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)C(C)(C)NC(C)=O)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001513351632.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513351632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513351632 none CO[C@@H]1CN(C(=O)C(C)(C)NC(C)=O)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 5, 11, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 13, 13, 13, 13, 13, 13, 26, 26, 36, 36, 36, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 13, 13, 36, 36, 36, 36, 36, 36, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 207 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351632 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351632/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351632 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 861) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/861 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/861' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)C(C)(C)NC(C)=O)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001513351632.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513351632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513351632 none CO[C@@H]1CN(C(=O)C(C)(C)NC(C)=O)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 5, 11, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 12, 12, 12, 12, 12, 12, 27, 27, 36, 36, 36, 50, 50, 50, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 12, 12, 36, 36, 36, 36, 36, 36, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 191 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351632 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513351632 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351632/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351632/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351632 Building ZINC001513351632 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351632' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351632 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513351632 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351632/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351632 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 860) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/860: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)C(C)(C)NC(C)=O)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001513351632.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513351632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513351632 none CO[C@@H]1CN(C(=O)C(C)(C)NC(C)=O)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 5, 11, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 13, 13, 13, 13, 13, 13, 26, 26, 36, 36, 36, 50, 50, 50, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 13, 13, 36, 36, 36, 36, 36, 36, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 207 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351632 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351632/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351632 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 861) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/861: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)C(C)(C)NC(C)=O)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001513351632.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513351632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513351632 none CO[C@@H]1CN(C(=O)C(C)(C)NC(C)=O)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 5, 11, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 12, 12, 12, 12, 12, 12, 27, 27, 36, 36, 36, 50, 50, 50, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 12, 12, 36, 36, 36, 36, 36, 36, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 191 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351632 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513351632 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351632/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351632/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351632 Building ZINC001513351656 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351656' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351656 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513351656 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351656/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351656 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/862 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)C2CN(C(C)=O)C2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001513351656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513351656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001513351656 none CO[C@@H]1CN(C(=O)C2CN(C(C)=O)C2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 5, 11, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 10, 10, 10, 10, 10, 10, 18, 18, 33, 33, 33, 50, 50, 33, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 10, 10, 33, 33, 33, 50, 50, 50, 33, 33, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351656 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351656/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351656 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 863) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/863 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/863' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)C2CN(C(C)=O)C2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001513351656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513351656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001513351656 none CO[C@@H]1CN(C(=O)C2CN(C(C)=O)C2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 5, 11, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 10, 10, 10, 10, 10, 19, 19, 32, 32, 32, 50, 50, 32, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 10, 10, 32, 32, 32, 50, 50, 50, 32, 32, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351656 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513351656 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351656/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351656/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351656 Building ZINC001513351656 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351656' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351656 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513351656 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351656/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351656 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 862) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/862: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)C2CN(C(C)=O)C2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001513351656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513351656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001513351656 none CO[C@@H]1CN(C(=O)C2CN(C(C)=O)C2)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 5, 11, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 10, 10, 10, 10, 10, 10, 18, 18, 33, 33, 33, 50, 50, 33, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 10, 10, 33, 33, 33, 50, 50, 50, 33, 33, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351656 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351656/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351656 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 863) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/863: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)C2CN(C(C)=O)C2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001513351656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513351656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001513351656 none CO[C@@H]1CN(C(=O)C2CN(C(C)=O)C2)C[C@H]1NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 5, 11, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 10, 10, 10, 10, 10, 19, 19, 32, 32, 32, 50, 50, 32, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 10, 10, 32, 32, 32, 50, 50, 50, 32, 32, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 43, 44, 45, 46, 47, 48, 49, 50, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351656 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513351656 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351656/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351656/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513351656 Building ZINC001513394379 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394379' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394379 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513394379 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394379/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394379 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/864 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](C)S(C)(=O)=O) `ZINC001513394379.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513394379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001513394379 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 11, 11, 11, 11, 6, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 27, 27, 27, 45, 45, 45, 50, 50, 50, 19, 19, 19, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 27, 45, 45, 45, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394379 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394379/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394379 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 865) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/865 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/865' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](C)S(C)(=O)=O) `ZINC001513394379.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513394379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394379/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001513394379 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 7, 7, 7, 4, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 20, 20, 20, 42, 42, 42, 50, 50, 50, 12, 12, 12, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 20, 42, 42, 42, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394379 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513394379 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394379/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394379/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394379 Building ZINC001513394379 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394379' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394379 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513394379 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394379/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394379 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 864) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/864: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](C)S(C)(=O)=O) `ZINC001513394379.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513394379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001513394379 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 11, 11, 11, 11, 6, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 27, 27, 27, 45, 45, 45, 50, 50, 50, 19, 19, 19, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 27, 45, 45, 45, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394379 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394379/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394379 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 865) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/865: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](C)S(C)(=O)=O) `ZINC001513394379.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513394379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394379/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001513394379 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@@H](C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 7, 7, 7, 4, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 20, 20, 20, 42, 42, 42, 50, 50, 50, 12, 12, 12, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 20, 42, 42, 42, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394379 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513394379 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394379/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394379/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394379 Building ZINC001513394389 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394389' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394389 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513394389 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394389/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394389 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/866 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](C)S(C)(=O)=O) `ZINC001513394389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513394389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001513394389 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 11, 11, 11, 4, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 26, 26, 26, 44, 44, 44, 50, 50, 50, 17, 17, 17, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 26, 44, 44, 44, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394389 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394389/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394389 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 867) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/867 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/867' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](C)S(C)(=O)=O) `ZINC001513394389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513394389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001513394389 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 20, 20, 20, 41, 41, 41, 50, 50, 50, 11, 11, 11, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 20, 41, 41, 41, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394389 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513394389 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394389/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394389/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394389 Building ZINC001513394389 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394389' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394389 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513394389 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394389/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394389 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 866) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/866: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](C)S(C)(=O)=O) `ZINC001513394389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513394389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001513394389 none CO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 11, 11, 11, 4, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 26, 26, 26, 44, 44, 44, 50, 50, 50, 17, 17, 17, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 26, 44, 44, 44, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394389 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394389/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394389 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 867) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/867: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](C)S(C)(=O)=O) `ZINC001513394389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513394389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001513394389 none CO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1NC(=O)[C@H](C)S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 20, 20, 20, 41, 41, 41, 50, 50, 50, 11, 11, 11, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 20, 41, 41, 41, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394389 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513394389 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394389/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394389/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513394389 Building ZINC001513404675 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513404675' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513404675 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513404675 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513404675/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513404675 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/868 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](NC(N)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001513404675.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513404675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513404675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001513404675 none CCC[C@@H](NC(N)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 29, 9, 29, 29, 39, 39, 39, 9, 9, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 8, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513404675 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513404675/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513404675 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 869) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/869 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/869' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](NC(N)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001513404675.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513404675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513404675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001513404675 none CCC[C@@H](NC(N)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 33, 10, 33, 33, 38, 38, 38, 10, 10, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513404675 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513404675 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513404675/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513404675/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513404675 Building ZINC001513404675 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513404675' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513404675 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513404675 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513404675/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513404675 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 868) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/868: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](NC(N)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001513404675.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513404675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513404675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001513404675 none CCC[C@@H](NC(N)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 29, 9, 29, 29, 39, 39, 39, 9, 9, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 8, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513404675 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513404675/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513404675 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 869) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/869: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](NC(N)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC) `ZINC001513404675.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513404675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513404675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001513404675 none CCC[C@@H](NC(N)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 33, 10, 33, 33, 38, 38, 38, 10, 10, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54, 55]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513404675 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513404675 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513404675/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513404675/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513404675 Building ZINC001513476711 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476711' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476711 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513476711 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476711/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476711 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/870 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)S(=O)(=O)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001513476711.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513476711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001513476711 none CC(C)S(=O)(=O)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 50, 27, 47, 47, 9, 6, 9, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 27, 27, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476711 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476711/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476711 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 871) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/871 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/871' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)S(=O)(=O)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001513476711.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513476711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476711/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001513476711 none CC(C)S(=O)(=O)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 50, 34, 45, 45, 10, 8, 10, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 34, 34, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 230 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476711 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513476711 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476711/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476711/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476711 Building ZINC001513476711 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476711' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476711 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513476711 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476711/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476711 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 870) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/870: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)S(=O)(=O)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001513476711.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513476711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001513476711 none CC(C)S(=O)(=O)CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 50, 27, 47, 47, 9, 6, 9, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 27, 27, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476711 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476711/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476711 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 871) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/871: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)S(=O)(=O)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001513476711.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513476711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476711/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001513476711 none CC(C)S(=O)(=O)CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 50, 34, 45, 45, 10, 8, 10, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 34, 34, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 230 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476711 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513476711 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476711/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476711/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476711 Building ZINC001513476731 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476731' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476731 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513476731 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476731/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476731 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/872 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@](C)(C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C) `ZINC001513476731.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513476731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001513476731 none CC(=O)N[C@@](C)(C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 41, 30, 41, 15, 30, 15, 15, 7, 15, 4, 1, 4, 1, 1, 1, 2, 2, 2, 15, 15, 15, 15, 41, 50, 50, 50, 50, 50, 50, 41, 41, 41, 15, 15, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 45, 15, 15, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 293 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476731 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476731/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476731 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 873) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/873 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/873' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@](C)(C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C) `ZINC001513476731.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513476731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476731/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001513476731 none CC(=O)N[C@@](C)(C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 43, 39, 43, 17, 39, 17, 17, 7, 17, 5, 1, 5, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17, 43, 50, 50, 50, 50, 50, 50, 43, 43, 43, 17, 17, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 51, 17, 17, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 257 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476731 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513476731 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476731/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476731/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476731 Building ZINC001513476731 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476731' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476731 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513476731 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476731/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476731 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 872) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/872: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@](C)(C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C) `ZINC001513476731.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513476731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001513476731 none CC(=O)N[C@@](C)(C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 41, 30, 41, 15, 30, 15, 15, 7, 15, 4, 1, 4, 1, 1, 1, 2, 2, 2, 15, 15, 15, 15, 41, 50, 50, 50, 50, 50, 50, 41, 41, 41, 15, 15, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 45, 15, 15, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 293 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476731 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476731/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476731 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 873) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/873: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@@](C)(C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C) `ZINC001513476731.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513476731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476731/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001513476731 none CC(=O)N[C@@](C)(C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 43, 39, 43, 17, 39, 17, 17, 7, 17, 5, 1, 5, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17, 43, 50, 50, 50, 50, 50, 50, 43, 43, 43, 17, 17, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 51, 17, 17, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 257 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476731 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513476731 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476731/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476731/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476731 Building ZINC001513476732 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476732' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476732 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513476732 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476732/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476732 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/874 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@](C)(C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C) `ZINC001513476732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513476732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001513476732 none CC(=O)N[C@](C)(C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 44, 30, 44, 13, 30, 13, 13, 5, 13, 3, 1, 3, 1, 1, 1, 2, 2, 2, 13, 13, 13, 13, 44, 50, 50, 50, 50, 50, 50, 44, 44, 44, 13, 13, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 39, 13, 13, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 272 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476732 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476732/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476732 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 875) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/875 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/875' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@](C)(C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C) `ZINC001513476732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513476732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001513476732 none CC(=O)N[C@](C)(C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 46, 34, 46, 15, 34, 15, 15, 5, 15, 4, 1, 4, 1, 1, 1, 2, 2, 2, 15, 15, 15, 15, 46, 50, 50, 49, 49, 49, 49, 46, 46, 46, 15, 15, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 45, 15, 15, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 251 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476732 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513476732 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476732/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476732/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476732 Building ZINC001513476732 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476732' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476732 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513476732 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476732/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476732 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 874) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/874: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@](C)(C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C) `ZINC001513476732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513476732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001513476732 none CC(=O)N[C@](C)(C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 44, 30, 44, 13, 30, 13, 13, 5, 13, 3, 1, 3, 1, 1, 1, 2, 2, 2, 13, 13, 13, 13, 44, 50, 50, 50, 50, 50, 50, 44, 44, 44, 13, 13, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 39, 13, 13, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 272 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476732 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476732/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476732 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 875) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/875: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@](C)(C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C) `ZINC001513476732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513476732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001513476732 none CC(=O)N[C@](C)(C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 46, 34, 46, 15, 34, 15, 15, 5, 15, 4, 1, 4, 1, 1, 1, 2, 2, 2, 15, 15, 15, 15, 46, 50, 50, 49, 49, 49, 49, 46, 46, 46, 15, 15, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 45, 15, 15, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 251 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476732 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513476732 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476732/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476732/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476732 Building ZINC001513476770 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476770' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476770 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513476770 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476770/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476770 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/876 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1) `ZINC001513476770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513476770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001513476770 none COCCn1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 49, 28, 28, 28, 12, 9, 12, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 28, 28, 50, 50, 50, 50, 50, 49, 49, 28, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 28] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 201 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476770 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476770/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476770 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 877) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/877 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/877' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1) `ZINC001513476770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513476770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001513476770 none COCCn1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 49, 25, 25, 25, 10, 6, 10, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 25, 25, 50, 50, 50, 50, 50, 49, 49, 25, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6, 25] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476770 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513476770 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476770/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476770/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476770 Building ZINC001513476770 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476770' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476770 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513476770 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476770/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476770 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 876) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/876: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1) `ZINC001513476770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513476770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001513476770 none COCCn1cc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 49, 28, 28, 28, 12, 9, 12, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 28, 28, 50, 50, 50, 50, 50, 49, 49, 28, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 28] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 201 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476770 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476770/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476770 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 877) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/877: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1) `ZINC001513476770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513476770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001513476770 none COCCn1cc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 49, 25, 25, 25, 10, 6, 10, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 25, 25, 50, 50, 50, 50, 50, 49, 49, 25, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6, 25] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476770 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513476770 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476770/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476770/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476770 Building ZINC001513476792 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476792' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476792 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513476792 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476792/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476792 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/878 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccnc1COCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001513476792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513476792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001513476792 none Cn1ccnc1COCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 12, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 44, 25, 9, 8, 9, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 25, 25, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476792 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476792/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476792 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 879) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/879 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/879' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccnc1COCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001513476792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513476792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001513476792 none Cn1ccnc1COCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 12, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 42, 19, 6, 5, 6, 5, 5, 3, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 19, 19, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476792 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513476792 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476792/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476792/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476792 Building ZINC001513476792 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476792' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476792 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513476792 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476792/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476792 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 878) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/878: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccnc1COCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001513476792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513476792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001513476792 none Cn1ccnc1COCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 12, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 44, 25, 9, 8, 9, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 25, 25, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476792 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476792/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476792 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 879) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/879: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccnc1COCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001513476792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513476792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001513476792 none Cn1ccnc1COCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 12, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 42, 19, 6, 5, 6, 5, 5, 3, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 19, 19, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5] 150 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476792 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513476792 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476792/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476792/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513476792 Building ZINC001513477108 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477108' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477108 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513477108 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477108/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477108 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/880 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccn(CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(=O)c1) `ZINC001513477108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513477108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001513477108 none Cc1ccn(CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 38, 11, 8, 11, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50] 150 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 189 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477108 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477108/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477108 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 881) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/881 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/881' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccn(CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(=O)c1) `ZINC001513477108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513477108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001513477108 none Cc1ccn(CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 38, 12, 9, 12, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 50] 150 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 185 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477108 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513477108 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477108/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477108/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477108 Building ZINC001513477108 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477108' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477108 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513477108 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477108/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477108 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 880) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/880: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccn(CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(=O)c1) `ZINC001513477108.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513477108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001513477108 none Cc1ccn(CC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 38, 11, 8, 11, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8, 50] 150 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 189 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477108 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477108/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477108 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 881) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/881: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccn(CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(=O)c1) `ZINC001513477108.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513477108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001513477108 none Cc1ccn(CC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)c(=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 38, 12, 9, 12, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 50] 150 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 185 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477108 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513477108 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477108/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477108/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477108 Building ZINC001513477114 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477114' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477114 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513477114 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477114/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477114 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/882 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnc3ccnn32)C[C@@H]1O) `ZINC001513477114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513477114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001513477114 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnc3ccnn32)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 40, 40, 50, 50, 48, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 169 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477114 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477114/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477114 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 883) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/883 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/883' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnc3ccnn32)C[C@@H]1O) `ZINC001513477114.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513477114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001513477114 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnc3ccnn32)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 35, 35, 50, 50, 48, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477114 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513477114 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477114/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477114/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477114 Building ZINC001513477114 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477114' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477114 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513477114 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477114/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477114 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 882) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/882: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnc3ccnn32)C[C@@H]1O) `ZINC001513477114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513477114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001513477114 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnc3ccnn32)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 40, 40, 50, 50, 48, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 169 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477114 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477114/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477114 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 883) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/883: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnc3ccnn32)C[C@@H]1O) `ZINC001513477114.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513477114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001513477114 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccnc3ccnn32)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 35, 35, 50, 50, 48, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477114 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513477114 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477114/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477114/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477114 Building ZINC001513477165 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477165' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477165 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513477165 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477165/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477165 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/884 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CCC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001513477165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513477165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001513477165 none Cc1noc(CCC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', '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, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 24, 20, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 24, 24, 20, 20, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477165 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477165/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477165 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 885) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/885 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/885' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CCC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001513477165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513477165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001513477165 none Cc1noc(CCC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', '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, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 26, 22, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 26, 26, 22, 22, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 147 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477165 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513477165 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477165/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477165/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477165 Building ZINC001513477165 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477165' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477165 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513477165 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477165/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477165 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 884) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/884: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CCC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001513477165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513477165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001513477165 none Cc1noc(CCC(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', '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, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 24, 20, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 24, 24, 20, 20, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477165 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477165/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477165 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 885) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/885: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CCC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001513477165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513477165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001513477165 none Cc1noc(CCC(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', '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, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 26, 22, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 26, 26, 22, 22, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 147 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477165 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513477165 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477165/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477165/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477165 Building ZINC001513477187 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477187' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477187 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513477187 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477187/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477187 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/886 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCC1) `ZINC001513477187.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513477187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001513477187 none CNC(=O)C1(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 41, 50, 31, 11, 31, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 41, 41, 41, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 41, 41, 41, 41, 41, 41] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 192 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477187 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477187/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477187 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 887) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/887 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/887' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCC1) `ZINC001513477187.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513477187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477187/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001513477187 none CNC(=O)C1(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 46, 50, 34, 12, 34, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 46, 46, 46, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 46, 46, 46, 46, 46, 46] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477187 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513477187 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477187/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477187/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477187 Building ZINC001513477187 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477187' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477187 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513477187 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477187/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477187 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 886) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/886: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCC1) `ZINC001513477187.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513477187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001513477187 none CNC(=O)C1(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 41, 50, 31, 11, 31, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 41, 41, 41, 50, 50, 50, 50, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 41, 41, 41, 41, 41, 41] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 192 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477187 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477187/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477187 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 887) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/887: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCC1) `ZINC001513477187.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513477187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477187/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001513477187 none CNC(=O)C1(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 46, 50, 34, 12, 34, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 46, 46, 46, 50, 50, 50, 50, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 12, 12, 46, 46, 46, 46, 46, 46] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477187 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513477187 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477187/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477187/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477187 Building ZINC001513477235 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477235' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513477235 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477235/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/888 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(C(N)=O)s2)C[C@@H]1O) `ZINC001513477235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513477235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001513477235 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(C(N)=O)s2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'S.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 14, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 23, 23, 48, 48, 48, 48, 50, 50, 48, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 48, 48, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 144 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477235/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 889) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/889 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/889' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(C(N)=O)s2)C[C@@H]1O) `ZINC001513477235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513477235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001513477235 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(C(N)=O)s2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'S.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 14, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 24, 24, 43, 43, 43, 43, 50, 50, 43, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 43, 43, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513477235 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477235/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477235/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477235 Building ZINC001513477235 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477235' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513477235 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477235/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 888) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/888: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(C(N)=O)s2)C[C@@H]1O) `ZINC001513477235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513477235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001513477235 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(C(N)=O)s2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'S.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 14, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 23, 23, 48, 48, 48, 48, 50, 50, 48, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 48, 48, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 144 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477235/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 889) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/889: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(C(N)=O)s2)C[C@@H]1O) `ZINC001513477235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513477235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001513477235 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)c2ccc(C(N)=O)s2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'S.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 14, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 24, 24, 43, 43, 43, 43, 50, 50, 43, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 43, 43, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477235 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513477235 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477235/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477235/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477235 Building ZINC001513477244 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477244' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477244 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513477244 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477244/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477244 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/890 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCOC[C@H]2CCCO2)C[C@@H]1O) `ZINC001513477244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513477244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001513477244 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCOC[C@H]2CCCO2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 18, 19, 36, 45, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 18, 18, 19, 19, 45, 45, 50, 50, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 184 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477244 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477244/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477244 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 891) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/891 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/891' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCOC[C@H]2CCCO2)C[C@@H]1O) `ZINC001513477244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513477244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001513477244 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCOC[C@H]2CCCO2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 16, 16, 34, 49, 50, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 16, 16, 16, 16, 46, 46, 50, 50, 50, 50, 50, 50, 5, 5, 15] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477244 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513477244 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477244/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477244/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477244 Building ZINC001513477244 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477244' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477244 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513477244 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477244/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477244 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 890) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/890: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCOC[C@H]2CCCO2)C[C@@H]1O) `ZINC001513477244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513477244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001513477244 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCOC[C@H]2CCCO2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 18, 19, 36, 45, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 18, 18, 19, 19, 45, 45, 50, 50, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 184 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477244 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477244/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477244 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 891) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/891: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCOC[C@H]2CCCO2)C[C@@H]1O) `ZINC001513477244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513477244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001513477244 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCOC[C@H]2CCCO2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 16, 16, 34, 49, 50, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 16, 16, 16, 16, 46, 46, 50, 50, 50, 50, 50, 50, 5, 5, 15] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477244 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513477244 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477244/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477244/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477244 Building ZINC001513477248 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477248' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477248 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513477248 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477248/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477248 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/892 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCOC[C@@H]2CCCO2)C[C@@H]1O) `ZINC001513477248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513477248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001513477248 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCOC[C@@H]2CCCO2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 21, 21, 39, 45, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 21, 21, 21, 21, 45, 45, 50, 50, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 172 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477248 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477248/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477248 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 893) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/893 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/893' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCOC[C@@H]2CCCO2)C[C@@H]1O) `ZINC001513477248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513477248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001513477248 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCOC[C@@H]2CCCO2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 14, 14, 31, 47, 50, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 14, 14, 14, 14, 46, 46, 50, 50, 50, 50, 50, 50, 5, 5, 15] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477248 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513477248 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477248/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477248/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477248 Building ZINC001513477248 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477248' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477248 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513477248 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477248/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477248 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 892) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/892: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCOC[C@@H]2CCCO2)C[C@@H]1O) `ZINC001513477248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513477248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001513477248 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCOC[C@@H]2CCCO2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 21, 21, 39, 45, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 21, 21, 21, 21, 45, 45, 50, 50, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 172 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477248 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477248/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477248 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 893) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/893: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCOC[C@@H]2CCCO2)C[C@@H]1O) `ZINC001513477248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513477248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001513477248 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCOC[C@@H]2CCCO2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 14, 14, 31, 47, 50, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 14, 14, 14, 14, 46, 46, 50, 50, 50, 50, 50, 50, 5, 5, 15] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477248 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513477248 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477248/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477248/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477248 Building ZINC001513477650 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477650' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477650 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513477650 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477650/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477650 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/894 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CCCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001513477650.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513477650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513477650 none CN(C)C(=O)CCCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 37, 50, 28, 27, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 37, 37, 33, 33, 27, 27, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 252 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477650 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477650/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477650 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 895) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/895 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/895' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CCCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001513477650.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513477650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513477650 none CN(C)C(=O)CCCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 34, 50, 23, 20, 6, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 33, 33, 26, 26, 20, 20, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 235 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477650 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513477650 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477650/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477650/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477650 Building ZINC001513477650 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477650' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477650 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513477650 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477650/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477650 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 894) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/894: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CCCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001513477650.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513477650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513477650 none CN(C)C(=O)CCCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 37, 50, 28, 27, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 37, 37, 33, 33, 27, 27, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 252 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477650 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477650/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477650 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 895) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/895: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CCCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001513477650.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513477650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513477650 none CN(C)C(=O)CCCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 34, 50, 23, 20, 6, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 33, 33, 26, 26, 20, 20, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 6, 6] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 235 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477650 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513477650 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477650/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477650/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477650 Building ZINC001513477670 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477670' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477670 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513477670 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477670/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477670 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/896 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C(=O)CC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001513477670.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513477670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001513477670 none CC(C)N1C(=O)CC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 50, 48, 48, 48, 48, 48, 26, 48, 14, 26, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 48, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 193 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477670 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477670/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477670 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 897) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/897 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/897' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C(=O)CC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001513477670.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513477670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477670/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001513477670 none CC(C)N1C(=O)CC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 50, 49, 49, 49, 49, 49, 27, 49, 11, 27, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 186 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477670 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513477670 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477670/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477670/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477670 Building ZINC001513477670 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477670' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477670 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513477670 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477670/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477670 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 896) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/896: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C(=O)CC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001513477670.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513477670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001513477670 none CC(C)N1C(=O)CC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 50, 48, 48, 48, 48, 48, 26, 48, 14, 26, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 48, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 14, 14] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 193 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477670 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477670/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477670 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 897) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/897: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C(=O)CC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001513477670.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513477670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477670/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001513477670 none CC(C)N1C(=O)CC[C@H]1C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 50, 49, 49, 49, 49, 49, 27, 49, 11, 27, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11] 150 rigid atoms, others: [51, 49, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 52, 53, 54]) total number of confs: 186 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477670 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513477670 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477670/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477670/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477670 Building ZINC001513477704 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477704' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477704 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513477704 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477704/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477704 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/898 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CN2CCCCC2=O)C[C@@H]1O) `ZINC001513477704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513477704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513477704 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CN2CCCCC2=O)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 8, 5, 5, 5, 5, 1, 11, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 11, 11, 42, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 186 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477704 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477704/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477704 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 899) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/899 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/899' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CN2CCCCC2=O)C[C@@H]1O) `ZINC001513477704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513477704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513477704 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CN2CCCCC2=O)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 8, 5, 5, 5, 5, 1, 11, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 11, 11, 40, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 180 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477704 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513477704 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477704/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477704/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477704 Building ZINC001513477704 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477704' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477704 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513477704 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477704/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477704 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 898) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/898: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CN2CCCCC2=O)C[C@@H]1O) `ZINC001513477704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513477704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513477704 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CN2CCCCC2=O)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 8, 5, 5, 5, 5, 1, 11, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 11, 11, 42, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 186 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477704 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477704/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477704 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 899) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/899: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CN2CCCCC2=O)C[C@@H]1O) `ZINC001513477704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513477704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513477704 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CN2CCCCC2=O)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 8, 5, 5, 5, 5, 1, 11, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 11, 11, 40, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 180 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477704 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513477704 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477704/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477704/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477704 Building ZINC001513477721 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477721' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477721 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513477721 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477721/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477721 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/900 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CN3CCC2CC3)C[C@@H]1O) `ZINC001513477721.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513477721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513477721 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CN3CCC2CC3)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 14, 14, 14, 14, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 42] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 185 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477721 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477721/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477721 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 901) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/901 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/901' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CN3CCC2CC3)C[C@@H]1O) `ZINC001513477721.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513477721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477721/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513477721 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CN3CCC2CC3)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 5, 16, 16, 16, 16, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 48] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 195 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477721 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513477721 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477721/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477721/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477721 Building ZINC001513477721 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477721' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477721 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513477721 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477721/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477721 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 900) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/900: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CN3CCC2CC3)C[C@@H]1O) `ZINC001513477721.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513477721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513477721 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CN3CCC2CC3)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 14, 14, 14, 14, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 42] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 185 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477721 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477721/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477721 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 901) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/901: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CN3CCC2CC3)C[C@@H]1O) `ZINC001513477721.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513477721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477721/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513477721 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CN3CCC2CC3)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 5, 16, 16, 16, 16, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 48] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 195 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477721 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513477721 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477721/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477721/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477721 Building ZINC001513477722 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477722' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477722 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513477722 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477722/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477722 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/902 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CN3CCC2CC3)C[C@@H]1O) `ZINC001513477722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513477722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513477722 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CN3CCC2CC3)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 16, 16, 16, 16, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 48] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 187 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477722 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477722/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477722 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 903) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/903 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/903' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CN3CCC2CC3)C[C@@H]1O) `ZINC001513477722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513477722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513477722 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CN3CCC2CC3)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 5, 15, 15, 15, 15, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 45] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 194 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477722 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513477722 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477722/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477722/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477722 Building ZINC001513477722 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477722' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477722 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513477722 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477722/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477722 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 902) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/902: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CN3CCC2CC3)C[C@@H]1O) `ZINC001513477722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513477722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513477722 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CN3CCC2CC3)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 16, 16, 16, 16, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 48] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 187 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477722 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477722/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477722 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 903) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/903: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CN3CCC2CC3)C[C@@H]1O) `ZINC001513477722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513477722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513477722 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CN3CCC2CC3)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 3, 3, 5, 15, 15, 15, 15, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 45] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 194 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477722 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513477722 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477722/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477722/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477722 Building ZINC001513477744 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477744' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477744 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513477744 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477744/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477744 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/904 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COC2CCOCC2)C[C@@H]1O) `ZINC001513477744.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513477744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513477744 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COC2CCOCC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 6, 6, 6, 6, 6, 6, 18, 48, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 132 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477744 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477744/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477744 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 905) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/905 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/905' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COC2CCOCC2)C[C@@H]1O) `ZINC001513477744.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513477744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477744/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513477744 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COC2CCOCC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 16, 49, 50, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 15] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477744 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513477744 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477744/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477744/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477744 Building ZINC001513477744 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477744' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477744 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513477744 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477744/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477744 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 904) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/904: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COC2CCOCC2)C[C@@H]1O) `ZINC001513477744.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513477744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513477744 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COC2CCOCC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 6, 6, 6, 6, 6, 6, 18, 48, 50, 50, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 18] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 132 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477744 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477744/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477744 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 905) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/905: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COC2CCOCC2)C[C@@H]1O) `ZINC001513477744.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513477744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477744/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513477744 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)COC2CCOCC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 16, 49, 50, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 5, 15] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477744 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513477744 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477744/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477744/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513477744 Building ZINC001513478020 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478020' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478020 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513478020 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478020/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478020 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/906 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCCCN2C(N)=O)C[C@@H]1O) `ZINC001513478020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513478020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513478020 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCCCN2C(N)=O)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 8, 1, 8, 11, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 28, 40, 46, 46, 46, 46, 46, 46, 46, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 46, 46, 46, 46, 46, 46, 46, 46, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 164 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478020 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478020/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478020 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 907) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/907 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/907' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCCCN2C(N)=O)C[C@@H]1O) `ZINC001513478020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513478020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513478020 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCCCN2C(N)=O)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 8, 1, 8, 11, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 29, 37, 46, 46, 46, 46, 46, 46, 46, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 46, 46, 46, 46, 46, 46, 46, 46, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 179 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478020 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513478020 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478020/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478020/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478020 Building ZINC001513478020 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478020' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478020 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513478020 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478020/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478020 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 906) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/906: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCCCN2C(N)=O)C[C@@H]1O) `ZINC001513478020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513478020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513478020 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCCCN2C(N)=O)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 8, 1, 8, 11, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 28, 40, 46, 46, 46, 46, 46, 46, 46, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 46, 46, 46, 46, 46, 46, 46, 46, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 164 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478020 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478020/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478020 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 907) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/907: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCCCN2C(N)=O)C[C@@H]1O) `ZINC001513478020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513478020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513478020 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCCCN2C(N)=O)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 8, 1, 8, 11, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 29, 37, 46, 46, 46, 46, 46, 46, 46, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 46, 46, 46, 46, 46, 46, 46, 46, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 179 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478020 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513478020 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478020/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478020/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478020 Building ZINC001513478024 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478024' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478024 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513478024 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478024/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478024 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/908 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCCCN2C(N)=O)C[C@@H]1O) `ZINC001513478024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513478024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513478024 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCCCN2C(N)=O)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 8, 1, 8, 11, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 25, 36, 46, 46, 46, 46, 46, 46, 46, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 46, 46, 46, 46, 46, 46, 46, 46, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 174 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478024 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478024/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478024 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 909) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/909 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/909' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCCCN2C(N)=O)C[C@@H]1O) `ZINC001513478024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513478024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513478024 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCCCN2C(N)=O)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 8, 1, 8, 11, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 27, 34, 43, 43, 43, 43, 43, 43, 43, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 43, 43, 43, 43, 43, 43, 43, 43, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 185 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478024 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513478024 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478024/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478024/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478024 Building ZINC001513478024 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478024' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478024 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513478024 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478024/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478024 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 908) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/908: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCCCN2C(N)=O)C[C@@H]1O) `ZINC001513478024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513478024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513478024 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCCCN2C(N)=O)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 8, 1, 8, 11, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 25, 36, 46, 46, 46, 46, 46, 46, 46, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 46, 46, 46, 46, 46, 46, 46, 46, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 174 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478024 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478024/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478024 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 909) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/909: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCCCN2C(N)=O)C[C@@H]1O) `ZINC001513478024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513478024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513478024 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCCCN2C(N)=O)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 8, 1, 8, 11, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 27, 34, 43, 43, 43, 43, 43, 43, 43, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 43, 43, 43, 43, 43, 43, 43, 43, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 185 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478024 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513478024 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478024/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478024/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478024 Building ZINC001513478160 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478160' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478160 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513478160 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478160/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478160 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/910 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3nc[nH]c3C2)C[C@@H]1O) `ZINC001513478160.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513478160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513478160 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3nc[nH]c3C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 8, 6, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 24, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 173 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478160 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478160/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478160 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 911) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/911 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/911' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3nc[nH]c3C2)C[C@@H]1O) `ZINC001513478160.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513478160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513478160 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3nc[nH]c3C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 8, 6, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 25, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 179 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478160 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513478160 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478160/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478160/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478160 Building ZINC001513478160 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478160' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478160 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513478160 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478160/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478160 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 910) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/910: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3nc[nH]c3C2)C[C@@H]1O) `ZINC001513478160.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513478160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513478160 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3nc[nH]c3C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 8, 6, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 24, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 173 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478160 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478160/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478160 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 911) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/911: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3nc[nH]c3C2)C[C@@H]1O) `ZINC001513478160.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513478160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513478160 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3nc[nH]c3C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 8, 6, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 25, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 179 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478160 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513478160 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478160/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478160/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478160 Building ZINC001513478162 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478162' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478162 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513478162 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478162/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478162 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/912 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3nc[nH]c3C2)C[C@@H]1O) `ZINC001513478162.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513478162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513478162 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3nc[nH]c3C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 8, 6, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 24, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 178 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478162 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478162/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478162 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 913) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/913 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/913' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3nc[nH]c3C2)C[C@@H]1O) `ZINC001513478162.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513478162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513478162 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3nc[nH]c3C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 8, 6, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 23, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478162 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513478162 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478162/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478162/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478162 Building ZINC001513478162 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478162' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478162 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513478162 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478162/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478162 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 912) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/912: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3nc[nH]c3C2)C[C@@H]1O) `ZINC001513478162.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513478162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513478162 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3nc[nH]c3C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 8, 6, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 24, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 178 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478162 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478162/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478162 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 913) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/913: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3nc[nH]c3C2)C[C@@H]1O) `ZINC001513478162.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513478162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513478162 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3nc[nH]c3C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 8, 6, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 23, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478162 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513478162 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478162/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478162/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478162 Building ZINC001513478171 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478171' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478171 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513478171 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478171/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478171 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/914 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)N1CCCC1=O) `ZINC001513478171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513478171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001513478171 none C[C@H](CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 38, 48, 15, 13, 15, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 48, 50, 50, 50, 50, 50, 48, 48, 48, 38, 38, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478171 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478171/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478171 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 915) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/915 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/915' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)N1CCCC1=O) `ZINC001513478171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513478171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001513478171 none C[C@H](CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 38, 42, 14, 13, 14, 13, 13, 3, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 42, 50, 50, 50, 50, 50, 42, 42, 42, 38, 38, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 218 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478171 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513478171 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478171/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478171/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478171 Building ZINC001513478171 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478171' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478171 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513478171 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478171/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478171 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 914) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/914: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)N1CCCC1=O) `ZINC001513478171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513478171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001513478171 none C[C@H](CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 38, 48, 15, 13, 15, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 48, 50, 50, 50, 50, 50, 48, 48, 48, 38, 38, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478171 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478171/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478171 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 915) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/915: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)N1CCCC1=O) `ZINC001513478171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513478171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001513478171 none C[C@H](CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 38, 42, 14, 13, 14, 13, 13, 3, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 42, 50, 50, 50, 50, 50, 42, 42, 42, 38, 38, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 218 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478171 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513478171 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478171/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478171/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478171 Building ZINC001513478172 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478172' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478172 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513478172 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478172/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478172 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/916 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)N1CCCC1=O) `ZINC001513478172.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513478172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001513478172 none C[C@@H](CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [41, 30, 41, 10, 9, 10, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 41, 50, 50, 50, 50, 50, 41, 41, 41, 30, 30, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478172 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478172/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478172 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 917) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/917 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/917' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)N1CCCC1=O) `ZINC001513478172.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513478172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478172/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001513478172 none C[C@@H](CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 34, 42, 14, 13, 14, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 42, 50, 50, 50, 50, 50, 42, 42, 42, 34, 34, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 223 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478172 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513478172 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478172/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478172/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478172 Building ZINC001513478172 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478172' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478172 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513478172 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478172/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478172 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 916) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/916: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)N1CCCC1=O) `ZINC001513478172.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513478172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001513478172 none C[C@@H](CC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [41, 30, 41, 10, 9, 10, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 41, 50, 50, 50, 50, 50, 41, 41, 41, 30, 30, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478172 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478172/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478172 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 917) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/917: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)N1CCCC1=O) `ZINC001513478172.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513478172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478172/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001513478172 none C[C@@H](CC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 34, 42, 14, 13, 14, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 42, 50, 50, 50, 50, 50, 42, 42, 42, 34, 34, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 13, 13, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 223 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478172 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513478172 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478172/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478172/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478172 Building ZINC001513478408 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478408' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478408 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513478408 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478408/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478408 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/918 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3nncn3C2)C[C@@H]1O) `ZINC001513478408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513478408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001513478408 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3nncn3C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 22, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 163 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478408 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478408/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478408 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 919) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/919 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/919' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3nncn3C2)C[C@@H]1O) `ZINC001513478408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513478408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001513478408 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3nncn3C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 25, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 175 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478408 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513478408 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478408/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478408/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478408 Building ZINC001513478408 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478408' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478408 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513478408 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478408/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478408 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 918) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/918: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3nncn3C2)C[C@@H]1O) `ZINC001513478408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513478408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001513478408 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3nncn3C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 22, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 163 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478408 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478408/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478408 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 919) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/919: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3nncn3C2)C[C@@H]1O) `ZINC001513478408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513478408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001513478408 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CCc3nncn3C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 25, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 175 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478408 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513478408 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478408/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478408/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478408 Building ZINC001513478412 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478412' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478412 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513478412 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478412/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478412 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/920 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3nncn3C2)C[C@@H]1O) `ZINC001513478412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513478412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001513478412 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3nncn3C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 24, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 168 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478412 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478412/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478412 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 921) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/921 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/921' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3nncn3C2)C[C@@H]1O) `ZINC001513478412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513478412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001513478412 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3nncn3C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 22, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 171 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478412 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513478412 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478412/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478412/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478412 Building ZINC001513478412 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478412' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478412 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513478412 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478412/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478412 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 920) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/920: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3nncn3C2)C[C@@H]1O) `ZINC001513478412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513478412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001513478412 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3nncn3C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 24, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 168 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478412 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478412/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478412 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 921) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/921: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3nncn3C2)C[C@@H]1O) `ZINC001513478412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513478412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001513478412 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2CCc3nncn3C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 22, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 171 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478412 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513478412 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478412/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478412/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478412 Building ZINC001513478633 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478633' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478633 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513478633 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478633/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478633 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/922 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCn2ccccc2=O)C[C@@H]1O) `ZINC001513478633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513478633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001513478633 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCn2ccccc2=O)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 15, 15, 38, 43, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 38, 38, 43, 43, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 219 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478633 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478633/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478633 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 923) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/923 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/923' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCn2ccccc2=O)C[C@@H]1O) `ZINC001513478633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513478633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001513478633 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCn2ccccc2=O)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 17, 17, 40, 42, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 40, 40, 42, 42, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478633 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513478633 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478633/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478633/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478633 Building ZINC001513478633 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478633' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478633 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513478633 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478633/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478633 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 922) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/922: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCn2ccccc2=O)C[C@@H]1O) `ZINC001513478633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513478633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001513478633 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCn2ccccc2=O)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 15, 15, 38, 43, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 38, 38, 43, 43, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 219 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478633 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478633/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478633 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 923) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/923: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCn2ccccc2=O)C[C@@H]1O) `ZINC001513478633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513478633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001513478633 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)CCn2ccccc2=O)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 17, 17, 40, 42, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 40, 40, 42, 42, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478633 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513478633 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478633/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478633/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478633 Building ZINC001513478956 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478956' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478956 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513478956 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478956/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478956 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/924 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)N1CCOCC1) `ZINC001513478956.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513478956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513478956 none C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [43, 22, 43, 10, 22, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 43, 50, 50, 50, 50, 50, 43, 43, 43, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 205 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478956 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478956/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478956 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 925) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/925 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/925' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)N1CCOCC1) `ZINC001513478956.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513478956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478956/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513478956 none C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 23, 45, 10, 23, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 45, 50, 50, 50, 50, 50, 45, 45, 45, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 207 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478956 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513478956 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478956/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478956/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478956 Building ZINC001513478956 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478956' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478956 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513478956 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478956/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478956 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 924) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/924: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)N1CCOCC1) `ZINC001513478956.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513478956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513478956 none C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [43, 22, 43, 10, 22, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 43, 50, 50, 50, 50, 50, 43, 43, 43, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 205 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478956 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478956/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478956 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 925) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/925: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)N1CCOCC1) `ZINC001513478956.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513478956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478956/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513478956 none C[C@@H](C(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [45, 23, 45, 10, 23, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 45, 50, 50, 50, 50, 50, 45, 45, 45, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 207 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478956 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513478956 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478956/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478956/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478956 Building ZINC001513478974 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478974' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478974 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513478974 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478974/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478974 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/926 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001513478974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513478974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513478974 none CNC(=O)CCCCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 38, 50, 25, 21, 20, 5, 5, 5, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 38, 38, 25, 25, 23, 23, 20, 20, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 241 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478974 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478974/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478974 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 927) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/927 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/927' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001513478974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513478974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513478974 none CNC(=O)CCCCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 37, 50, 25, 20, 16, 3, 3, 3, 3, 3, 2, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 37, 37, 25, 25, 22, 22, 16, 16, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 3, 3] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478974 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513478974 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478974/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478974/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478974 Building ZINC001513478974 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478974' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478974 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513478974 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478974/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478974 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 926) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/926: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001513478974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513478974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513478974 none CNC(=O)CCCCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 38, 50, 25, 21, 20, 5, 5, 5, 5, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 38, 38, 25, 25, 23, 23, 20, 20, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 5, 5] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 241 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478974 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478974/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478974 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 927) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/927: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001513478974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513478974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513478974 none CNC(=O)CCCCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 37, 50, 25, 20, 16, 3, 3, 3, 3, 3, 2, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 37, 37, 25, 25, 22, 22, 16, 16, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 3, 3] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478974 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513478974 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478974/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478974/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513478974 Building ZINC001513479007 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479007' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479007 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513479007 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479007/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479007 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/928 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)C2)C[C@@H]1O) `ZINC001513479007.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513479007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513479007 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 25, 29, 48, 48, 48, 48, 48, 48, 50, 50, 48, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 48, 48, 48, 48, 50, 50, 48, 48, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 182 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479007 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479007/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479007 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 929) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/929 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/929' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)C2)C[C@@H]1O) `ZINC001513479007.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513479007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479007/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513479007 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 22, 26, 47, 47, 47, 47, 47, 47, 50, 50, 47, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 47, 47, 47, 47, 50, 50, 47, 47, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479007 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513479007 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479007/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479007/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479007 Building ZINC001513479007 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479007' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479007 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513479007 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479007/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479007 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 928) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/928: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)C2)C[C@@H]1O) `ZINC001513479007.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513479007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513479007 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 25, 29, 48, 48, 48, 48, 48, 48, 50, 50, 48, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 48, 48, 48, 48, 50, 50, 48, 48, 12, 12, 36] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 182 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479007 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479007/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479007 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 929) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/929: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)C2)C[C@@H]1O) `ZINC001513479007.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513479007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479007/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513479007 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@H]2CC[C@@H](C(N)=O)C2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 22, 26, 47, 47, 47, 47, 47, 47, 50, 50, 47, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 47, 47, 47, 47, 50, 50, 47, 47, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479007 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513479007 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479007/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479007/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479007 Building ZINC001513479012 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479012' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479012 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513479012 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479012/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479012 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/930 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001513479012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513479012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001513479012 none COCCn1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 43, 27, 27, 27, 27, 17, 8, 17, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 27, 50, 50, 50, 50, 50, 43, 43, 27, 27, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 214 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479012 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479012/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479012 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 931) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/931 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/931' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001513479012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513479012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001513479012 none COCCn1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 43, 30, 30, 30, 30, 16, 8, 16, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 30, 50, 50, 50, 50, 50, 43, 43, 30, 30, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479012 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513479012 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479012/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479012/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479012 Building ZINC001513479012 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479012' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479012 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513479012 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479012/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479012 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 930) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/930: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001513479012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513479012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001513479012 none COCCn1ccc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 43, 27, 27, 27, 27, 17, 8, 17, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 27, 50, 50, 50, 50, 50, 43, 43, 27, 27, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 214 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479012 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479012/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479012 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 931) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/931: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCn1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1) `ZINC001513479012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513479012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001513479012 none COCCn1ccc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 43, 30, 30, 30, 30, 16, 8, 16, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 30, 50, 50, 50, 50, 50, 43, 43, 30, 30, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479012 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513479012 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479012/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479012/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479012 Building ZINC001513479016 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479016' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479016 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513479016 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479016/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479016 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/932 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@]2(C)CCC(=O)NC2)C[C@@H]1O) `ZINC001513479016.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513479016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513479016 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@]2(C)CCC(=O)NC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 7, 19, 19, 19, 19, 30, 43, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 57] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 195 number of broken/clashed sets: 132 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479016 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479016/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479016 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 933) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/933 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/933' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@]2(C)CCC(=O)NC2)C[C@@H]1O) `ZINC001513479016.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513479016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513479016 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@]2(C)CCC(=O)NC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 7, 16, 16, 16, 16, 28, 42, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 48] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 189 number of broken/clashed sets: 128 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479016 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513479016 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479016/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479016/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479016 Building ZINC001513479016 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479016' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479016 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513479016 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479016/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479016 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 932) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/932: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@]2(C)CCC(=O)NC2)C[C@@H]1O) `ZINC001513479016.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513479016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513479016 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@]2(C)CCC(=O)NC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 7, 19, 19, 19, 19, 30, 43, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 57] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 195 number of broken/clashed sets: 132 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479016 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479016/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479016 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 933) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/933: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@]2(C)CCC(=O)NC2)C[C@@H]1O) `ZINC001513479016.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513479016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513479016 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@]2(C)CCC(=O)NC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 7, 16, 16, 16, 16, 28, 42, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 48] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 189 number of broken/clashed sets: 128 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479016 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513479016 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479016/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479016/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479016 Building ZINC001513479017 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479017' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479017 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513479017 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479017/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479017 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/934 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@]2(C)CCC(=O)NC2)C[C@@H]1O) `ZINC001513479017.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513479017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513479017 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@]2(C)CCC(=O)NC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 6, 17, 17, 17, 17, 31, 40, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 51] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 197 number of broken/clashed sets: 135 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479017 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479017/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479017 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 935) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/935 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/935' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@]2(C)CCC(=O)NC2)C[C@@H]1O) `ZINC001513479017.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513479017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479017/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513479017 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@]2(C)CCC(=O)NC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 16, 16, 16, 16, 31, 42, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 48] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 133 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479017 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513479017 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479017/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479017/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479017 Building ZINC001513479017 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479017' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479017 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513479017 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479017/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479017 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 934) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@]2(C)CCC(=O)NC2)C[C@@H]1O) `ZINC001513479017.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513479017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513479017 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@]2(C)CCC(=O)NC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 6, 17, 17, 17, 17, 31, 40, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 51] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 197 number of broken/clashed sets: 135 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479017 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479017/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479017 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 935) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/935: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@]2(C)CCC(=O)NC2)C[C@@H]1O) `ZINC001513479017.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513479017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479017/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513479017 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@]2(C)CCC(=O)NC2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 16, 16, 16, 16, 31, 42, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 48] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 133 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479017 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513479017 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479017/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479017/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479017 Building ZINC001513479455 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479455' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479455 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513479455 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479455/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479455 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/936 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCCC(=O)N2)C[C@@H]1O) `ZINC001513479455.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513479455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513479455 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCCC(=O)N2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 9, 43, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 33, 33, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 180 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479455 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479455/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479455 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 937) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/937 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/937' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCCC(=O)N2)C[C@@H]1O) `ZINC001513479455.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513479455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513479455 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCCC(=O)N2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 13, 13, 39, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 33, 33, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479455 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513479455 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479455/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479455/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479455 Building ZINC001513479455 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479455' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479455 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513479455 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479455/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479455 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 936) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/936: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCCC(=O)N2)C[C@@H]1O) `ZINC001513479455.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513479455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513479455 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCCC(=O)N2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 9, 43, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 33, 33, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 180 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479455 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479455/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479455 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 937) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/937: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCCC(=O)N2)C[C@@H]1O) `ZINC001513479455.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513479455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513479455 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@@H]2CCCC(=O)N2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 13, 13, 39, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 33, 33, 50, 50, 50, 50, 50, 50, 50, 10, 10, 30] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479455 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513479455 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479455/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479455/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479455 Building ZINC001513479456 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479456' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479456 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513479456 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479456/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479456 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/938 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCCC(=O)N2)C[C@@H]1O) `ZINC001513479456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513479456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513479456 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCCC(=O)N2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 10, 10, 47, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 32, 32, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 167 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479456 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479456/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479456 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 939) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/939 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/939' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCCC(=O)N2)C[C@@H]1O) `ZINC001513479456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513479456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513479456 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCCC(=O)N2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 11, 11, 37, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 28, 28, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479456 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513479456 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479456/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479456/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479456 Building ZINC001513479456 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479456' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479456 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513479456 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479456/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479456 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 938) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/938: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCCC(=O)N2)C[C@@H]1O) `ZINC001513479456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513479456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513479456 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCCC(=O)N2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 10, 10, 47, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 32, 32, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 167 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479456 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479456/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479456 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 939) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/939: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCCC(=O)N2)C[C@@H]1O) `ZINC001513479456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513479456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513479456 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)C[C@H]2CCCC(=O)N2)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 11, 11, 37, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 28, 28, 50, 50, 50, 50, 50, 50, 50, 9, 9, 27] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479456 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513479456 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479456/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479456/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479456 Building ZINC001513479600 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479600' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479600 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513479600 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479600/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479600 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/940 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1CCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001513479600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513479600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513479600 none Cc1nn(C)cc1CCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 31, 29, 11, 8, 11, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 31, 31, 29, 29, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479600 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479600/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479600 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 941) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/941 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/941' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1CCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001513479600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513479600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513479600 none Cc1nn(C)cc1CCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 32, 31, 12, 10, 12, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 32, 32, 31, 31, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 180 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479600 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513479600 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479600/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479600/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479600 Building ZINC001513479600 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479600' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479600 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513479600 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479600/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479600 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 940) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/940: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1CCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001513479600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513479600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513479600 none Cc1nn(C)cc1CCC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 31, 29, 11, 8, 11, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 31, 31, 29, 29, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 8, 8] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479600 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479600/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479600 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 941) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/941: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)cc1CCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1) `ZINC001513479600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513479600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513479600 none Cc1nn(C)cc1CCC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 32, 31, 12, 10, 12, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 32, 32, 31, 31, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 10, 10] 150 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 180 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479600 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513479600 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479600/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479600/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479600 Building ZINC001513479618 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479618' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479618 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513479618 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479618/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479618 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/942 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cnc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1) `ZINC001513479618.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513479618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001513479618 none CCOc1cnc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', '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, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 46, 46, 46, 46, 25, 11, 25, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 46, 46, 50, 50, 50, 50, 50, 46, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 46] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479618 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479618/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479618 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 943) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/943 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/943' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cnc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1) `ZINC001513479618.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513479618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479618/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001513479618 none CCOc1cnc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', '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, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 46, 46, 46, 46, 24, 9, 24, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 46, 46, 50, 50, 50, 50, 50, 46, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 46] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 146 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479618 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513479618 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479618/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479618/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479618 Building ZINC001513479618 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479618' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479618 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513479618 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479618/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479618 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 942) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/942: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cnc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1) `ZINC001513479618.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513479618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001513479618 none CCOc1cnc(C(=O)N2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', '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, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 46, 46, 46, 46, 25, 11, 25, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 46, 46, 50, 50, 50, 50, 50, 46, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 11, 11, 46] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479618 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479618/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479618 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 943) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/943: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cnc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1) `ZINC001513479618.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513479618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479618/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001513479618 none CCOc1cnc(C(=O)N2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', '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, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 46, 46, 46, 46, 24, 9, 24, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 46, 46, 50, 50, 50, 50, 50, 46, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 9, 9, 46] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 146 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479618 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513479618 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479618/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479618/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479618 Building ZINC001513479649 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479649' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479649 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513479649 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479649/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479649 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/944 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2C[C@@H]3O[C@H]2[C@H]2C[C@H]23)C[C@@H]1O) `ZINC001513479649.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513479649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001513479649 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2C[C@@H]3O[C@H]2[C@H]2C[C@H]23)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 16, 16, 16, 16, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 16, 16, 50, 50, 50, 50, 16, 16, 48] 150 rigid atoms, others: [0, 1, 34, 3, 32, 37, 38, 33, 40, 39, 2, 35, 4, 6, 5, 36] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 203 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479649 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479649/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479649 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 945) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/945 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/945' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2C[C@@H]3O[C@H]2[C@H]2C[C@H]23)C[C@@H]1O) `ZINC001513479649.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513479649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479649/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001513479649 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2C[C@@H]3O[C@H]2[C@H]2C[C@H]23)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 34, 3, 32, 37, 38, 33, 40, 39, 2, 35, 4, 6, 5, 36] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 190 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479649 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513479649 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479649/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479649/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479649 Building ZINC001513479649 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479649' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479649 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513479649 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479649/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479649 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 944) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/944: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2C[C@@H]3O[C@H]2[C@H]2C[C@H]23)C[C@@H]1O) `ZINC001513479649.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513479649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001513479649 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2C[C@@H]3O[C@H]2[C@H]2C[C@H]23)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 16, 16, 16, 16, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 16, 16, 50, 50, 50, 50, 16, 16, 48] 150 rigid atoms, others: [0, 1, 34, 3, 32, 37, 38, 33, 40, 39, 2, 35, 4, 6, 5, 36] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 203 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479649 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479649/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479649 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 945) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/945: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2C[C@@H]3O[C@H]2[C@H]2C[C@H]23)C[C@@H]1O) `ZINC001513479649.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513479649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479649/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001513479649 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)[C@@H]2C[C@@H]3O[C@H]2[C@H]2C[C@H]23)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 50, 50, 50, 50, 11, 11, 33] 150 rigid atoms, others: [0, 1, 34, 3, 32, 37, 38, 33, 40, 39, 2, 35, 4, 6, 5, 36] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 190 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479649 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513479649 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479649/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479649/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513479649 Building ZINC001513518723 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513518723' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513518723 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513518723 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513518723/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513518723 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/946 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCOCC(F)F)[C@@H](O)C1) `ZINC001513518723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513518723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513518723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513518723 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCOCC(F)F)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 15, 15, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 6, 6, 6, 20, 26, 37, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 20, 20, 26, 26, 50, 50, 50, 9, 3, 3] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513518723 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513518723/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513518723 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 947) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/947 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/947' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCOCC(F)F)[C@@H](O)C1) `ZINC001513518723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513518723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513518723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513518723 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCOCC(F)F)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 15, 15, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 8, 8, 8, 19, 19, 35, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 19, 19, 19, 19, 50, 50, 50, 9, 3, 3] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 181 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513518723 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513518723 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513518723/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513518723/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513518723 Building ZINC001513518723 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513518723' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513518723 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513518723 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513518723/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513518723 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 946) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/946: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCOCC(F)F)[C@@H](O)C1) `ZINC001513518723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513518723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513518723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513518723 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCOCC(F)F)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 15, 15, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 6, 6, 6, 20, 26, 37, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 20, 20, 26, 26, 50, 50, 50, 9, 3, 3] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513518723 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513518723/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513518723 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 947) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/947: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCOCC(F)F)[C@@H](O)C1) `ZINC001513518723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513518723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513518723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001513518723 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCOCC(F)F)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 15, 15, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 8, 8, 8, 19, 19, 35, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 19, 19, 19, 19, 50, 50, 50, 9, 3, 3] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 181 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513518723 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513518723 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513518723/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513518723/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513518723 Building ZINC001513524499 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524499' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524499 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513524499 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524499/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524499 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/948 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cnc[nH]1)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001513524499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513524499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001513524499 none C[C@H](Cc1cnc[nH]1)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 22, 39, 39, 47, 50, 50, 50, 50, 50, 22, 22, 10, 10, 10, 10, 5, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 39, 39, 39, 47, 47, 50, 50, 22, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 30] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 210 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524499 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524499/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524499 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 949) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/949 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/949' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cnc[nH]1)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001513524499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513524499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001513524499 none C[C@H](Cc1cnc[nH]1)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 20, 39, 39, 47, 50, 50, 50, 50, 50, 20, 20, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 39, 39, 39, 47, 47, 50, 50, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 207 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524499 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513524499 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524499/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524499/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524499 Building ZINC001513524499 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524499' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524499 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513524499 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524499/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524499 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 948) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/948: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cnc[nH]1)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001513524499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513524499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001513524499 none C[C@H](Cc1cnc[nH]1)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 22, 39, 39, 47, 50, 50, 50, 50, 50, 22, 22, 10, 10, 10, 10, 5, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 39, 39, 39, 47, 47, 50, 50, 22, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 30] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 210 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524499 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524499/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524499 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 949) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/949: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cnc[nH]1)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001513524499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513524499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001513524499 none C[C@H](Cc1cnc[nH]1)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [39, 20, 39, 39, 47, 50, 50, 50, 50, 50, 20, 20, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 39, 39, 39, 47, 47, 50, 50, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 207 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524499 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513524499 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524499/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524499/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524499 Building ZINC001513524501 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524501' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524501 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513524501 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524501/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524501 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/950 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1cnc[nH]1)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001513524501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513524501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001513524501 none C[C@@H](Cc1cnc[nH]1)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 21, 40, 40, 46, 50, 50, 50, 50, 50, 21, 21, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 40, 40, 40, 46, 46, 50, 50, 21, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 24] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 213 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524501 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524501/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524501 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 951) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/951 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/951' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1cnc[nH]1)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001513524501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513524501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001513524501 none C[C@@H](Cc1cnc[nH]1)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [41, 19, 41, 41, 49, 50, 50, 50, 50, 50, 19, 19, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 41, 41, 41, 49, 49, 50, 50, 19, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 218 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524501 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513524501 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524501/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524501/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524501 Building ZINC001513524501 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524501' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524501 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513524501 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524501/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524501 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 950) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/950: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1cnc[nH]1)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001513524501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513524501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001513524501 none C[C@@H](Cc1cnc[nH]1)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 21, 40, 40, 46, 50, 50, 50, 50, 50, 21, 21, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 40, 40, 40, 46, 46, 50, 50, 21, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 24] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 213 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524501 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524501/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524501 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 951) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/951: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1cnc[nH]1)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001513524501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513524501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001513524501 none C[C@@H](Cc1cnc[nH]1)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 1, 8, 6, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [41, 19, 41, 41, 49, 50, 50, 50, 50, 50, 19, 19, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 41, 41, 41, 49, 49, 50, 50, 19, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21] 150 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 218 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524501 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513524501 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524501/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524501/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513524501 Building ZINC001513527746 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513527746' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513527746 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513527746 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513527746/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513527746 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/952 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001513527746.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513527746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513527746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001513527746 none CC[C@H](C)[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 36, 50, 48, 9, 36, 36, 40, 40, 40, 9, 9, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 40, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [50, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 249 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513527746 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513527746/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513527746 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 953) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/953 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/953' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001513527746.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513527746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513527746/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001513527746 none CC[C@H](C)[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 37, 50, 49, 11, 37, 37, 42, 42, 42, 11, 11, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 42, 42, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [50, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 240 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513527746 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513527746 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513527746/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513527746/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513527746 Building ZINC001513527746 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513527746' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513527746 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513527746 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513527746/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513527746 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 952) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/952: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001513527746.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513527746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513527746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001513527746 none CC[C@H](C)[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 36, 50, 48, 9, 36, 36, 40, 40, 40, 9, 9, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 40, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [50, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 249 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513527746 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513527746/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513527746 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 953) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/953: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001513527746.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513527746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513527746/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001513527746 none CC[C@H](C)[C@H](NC(C)=O)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 5, 11, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 37, 50, 49, 11, 37, 37, 42, 42, 42, 11, 11, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 42, 42, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [50, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 240 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513527746 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513527746 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513527746/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513527746/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513527746 Building ZINC001513542566 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513542566' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513542566 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513542566 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513542566/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513542566 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/954 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001513542566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513542566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513542566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513542566 none CNC(=O)CCCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 40, 50, 23, 18, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 40, 40, 23, 23, 23, 23, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3] 150 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 53]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513542566 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513542566/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513542566 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 955) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/955 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/955' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001513542566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513542566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513542566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513542566 none CNC(=O)CCCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 42, 50, 27, 21, 20, 6, 6, 6, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50, 50, 50, 42, 42, 27, 27, 27, 27, 20, 20, 6, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 268 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513542566 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513542566 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513542566/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513542566/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513542566 Building ZINC001513542566 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513542566' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513542566 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513542566 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513542566/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513542566 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 954) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/954: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001513542566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513542566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513542566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513542566 none CNC(=O)CCCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 40, 50, 23, 18, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 40, 40, 23, 23, 23, 23, 13, 13, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3] 150 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 53]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513542566 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513542566/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513542566 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 955) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/955: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001513542566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513542566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513542566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513542566 none CNC(=O)CCCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 42, 50, 27, 21, 20, 6, 6, 6, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50, 50, 50, 42, 42, 27, 27, 27, 27, 20, 20, 6, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 268 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513542566 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513542566 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513542566/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513542566/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513542566 Building ZINC001513558128 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558128' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558128 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513558128 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558128/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558128 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/956 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCOC[C@H]2CCCO2)[C@@H](O)C1) `ZINC001513558128.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513558128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001513558128 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCOC[C@H]2CCCO2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 9, 9, 9, 20, 20, 27, 46, 50, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 20, 20, 20, 20, 46, 46, 50, 50, 50, 50, 50, 50, 15, 5, 5] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 199 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558128 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558128/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558128 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 957) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/957 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/957' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCOC[C@H]2CCCO2)[C@@H](O)C1) `ZINC001513558128.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513558128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558128/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001513558128 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCOC[C@H]2CCCO2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 8, 8, 8, 21, 22, 31, 48, 50, 50, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 21, 21, 22, 22, 48, 48, 50, 50, 50, 50, 50, 50, 9, 3, 3] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 208 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558128 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513558128 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558128/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558128/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558128 Building ZINC001513558128 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558128' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558128 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513558128 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558128/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558128 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 956) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/956: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCOC[C@H]2CCCO2)[C@@H](O)C1) `ZINC001513558128.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513558128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001513558128 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCOC[C@H]2CCCO2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 9, 9, 9, 20, 20, 27, 46, 50, 50, 50, 50, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 20, 20, 20, 20, 46, 46, 50, 50, 50, 50, 50, 50, 15, 5, 5] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 199 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558128 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558128/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558128 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 957) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/957: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCOC[C@H]2CCCO2)[C@@H](O)C1) `ZINC001513558128.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513558128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558128/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001513558128 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCOC[C@H]2CCCO2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 8, 8, 8, 21, 22, 31, 48, 50, 50, 50, 50, 50, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 21, 21, 22, 22, 48, 48, 50, 50, 50, 50, 50, 50, 9, 3, 3] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 208 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558128 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513558128 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558128/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558128/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558128 Building ZINC001513558129 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558129' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558129 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513558129 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558129/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558129 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/958 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCOC[C@@H]2CCCO2)[C@@H](O)C1) `ZINC001513558129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513558129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001513558129 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCOC[C@@H]2CCCO2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 12, 12, 12, 24, 25, 30, 44, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 12, 24, 24, 25, 25, 44, 44, 50, 50, 50, 50, 50, 50, 21, 7, 7] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 215 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558129 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558129/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558129 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 959) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/959 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/959' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCOC[C@@H]2CCCO2)[C@@H](O)C1) `ZINC001513558129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513558129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001513558129 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCOC[C@@H]2CCCO2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 10, 10, 10, 24, 26, 36, 48, 50, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 24, 24, 26, 26, 47, 47, 50, 50, 50, 50, 50, 50, 12, 4, 4] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558129 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513558129 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558129/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558129/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558129 Building ZINC001513558129 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558129' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558129 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513558129 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558129/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558129 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 958) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/958: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCOC[C@@H]2CCCO2)[C@@H](O)C1) `ZINC001513558129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513558129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001513558129 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCOC[C@@H]2CCCO2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 12, 12, 12, 24, 25, 30, 44, 50, 50, 50, 50, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 12, 24, 24, 25, 25, 44, 44, 50, 50, 50, 50, 50, 50, 21, 7, 7] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 215 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558129 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558129/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558129 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 959) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/959: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCOC[C@@H]2CCCO2)[C@@H](O)C1) `ZINC001513558129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513558129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001513558129 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)CCOC[C@@H]2CCCO2)[C@@H](O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 10, 10, 10, 24, 26, 36, 48, 50, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 24, 24, 26, 26, 47, 47, 50, 50, 50, 50, 50, 50, 12, 4, 4] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558129 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513558129 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558129/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558129/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513558129 Building ZINC001513574813 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513574813' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513574813 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513574813 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513574813/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513574813 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/960 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001513574813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513574813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513574813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513574813 none CCNC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 34, 34, 34, 34, 21, 17, 7, 7, 7, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 34, 33, 34, 25, 25, 17, 17, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 280 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513574813 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513574813/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513574813 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 961) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/961 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/961' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001513574813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513574813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513574813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513574813 none CCNC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 33, 33, 33, 33, 25, 23, 8, 8, 8, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 33, 33, 33, 29, 29, 23, 23, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513574813 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513574813 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513574813/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513574813/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513574813 Building ZINC001513574813 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513574813' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513574813 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513574813 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513574813/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513574813 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 960) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/960: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001513574813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513574813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513574813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513574813 none CCNC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 34, 34, 34, 34, 21, 17, 7, 7, 7, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 50, 50, 50, 50, 50, 34, 33, 34, 25, 25, 17, 17, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 280 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513574813 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513574813/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513574813 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 961) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/961: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001513574813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513574813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513574813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001513574813 none CCNC(=O)CCCC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 33, 33, 33, 33, 25, 23, 8, 8, 8, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 50, 50, 33, 33, 33, 29, 29, 23, 23, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12] 150 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513574813 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513574813 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513574813/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513574813/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513574813 Building ZINC001513579236 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513579236' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513579236 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513579236 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513579236/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513579236 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/962 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@H](CC(C)C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001513579236.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513579236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513579236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001513579236 none CC(=O)N[C@H](CC(C)C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 49, 13, 49, 49, 50, 50, 50, 13, 13, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18] 150 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 202 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513579236 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513579236/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513579236 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 963) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/963 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/963' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@H](CC(C)C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001513579236.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513579236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513579236/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001513579236 none CC(=O)N[C@H](CC(C)C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 48, 16, 48, 48, 50, 50, 50, 16, 16, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 49, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 206 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513579236 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513579236 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513579236/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513579236/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513579236 Building ZINC001513579236 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513579236' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513579236 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001513579236 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513579236/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513579236 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 962) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/962: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@H](CC(C)C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001513579236.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001513579236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513579236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001513579236 none CC(=O)N[C@H](CC(C)C)C(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 49, 13, 49, 49, 50, 50, 50, 13, 13, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18] 150 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 202 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513579236 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513579236/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513579236 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 963) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/963: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N[C@H](CC(C)C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O) `ZINC001513579236.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001513579236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513579236/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001513579236 none CC(=O)N[C@H](CC(C)C)C(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 48, 16, 48, 48, 50, 50, 50, 16, 16, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 49, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15] 150 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 54, 55, 56]) total number of confs: 206 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513579236 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001513579236 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513579236/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513579236/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001513579236 Building ZINC001515179433 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515179433' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515179433 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515179433 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515179433/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515179433 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/964 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2NC(=O)CC(N)=O)cn1) `ZINC001515179433.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515179433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515179433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001515179433 none Cn1cc([C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2NC(=O)CC(N)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 10, 10, 27, 39, 39, 12, 12, 12, 12, 12, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 27, 27, 39, 39, 12] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515179433 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515179433/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515179433 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 965) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/965 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/965' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2NC(=O)CC(N)=O)cn1) `ZINC001515179433.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515179433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515179433/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001515179433 none Cn1cc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2NC(=O)CC(N)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 5, 5, 5, 5, 2, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 10, 10, 30, 37, 37, 16, 16, 16, 16, 16, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 30, 30, 37, 37, 16] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515179433 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001515179433 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515179433/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515179433/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515179433 Building ZINC001515179433 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515179433' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515179433 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515179433 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515179433/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515179433 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 964) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/964: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2NC(=O)CC(N)=O)cn1) `ZINC001515179433.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515179433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515179433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001515179433 none Cn1cc([C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]2NC(=O)CC(N)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 10, 10, 27, 39, 39, 12, 12, 12, 12, 12, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 27, 27, 39, 39, 12] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515179433 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515179433/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515179433 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 965) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/965: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2NC(=O)CC(N)=O)cn1) `ZINC001515179433.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515179433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515179433/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001515179433 none Cn1cc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]2NC(=O)CC(N)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 1, 8, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 5, 5, 5, 5, 2, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 10, 10, 30, 37, 37, 16, 16, 16, 16, 16, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 30, 30, 37, 37, 16] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515179433 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001515179433 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515179433/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515179433/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515179433 Building ZINC001515213725 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213725' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213725 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515213725 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213725/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213725 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/966 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cc1nc[nH]n1) `ZINC001515213725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515213725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001515213725 none CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cc1nc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 9, 19, 19, 19, 35, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 9, 19, 35, 35, 50] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213725 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213725/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213725 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 967) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/967 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/967' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cc1nc[nH]n1) `ZINC001515213725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515213725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001515213725 none CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cc1nc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 5, 5, 5, 5, 3, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 19, 19, 19, 34, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 14, 19, 34, 34, 50] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213725 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001515213725 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213725/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213725/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213725 Building ZINC001515213725 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213725' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213725 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515213725 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213725/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213725 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 966) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/966: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cc1nc[nH]n1) `ZINC001515213725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515213725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001515213725 none CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cc1nc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 9, 19, 19, 19, 35, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 9, 19, 35, 35, 50] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213725 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213725/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213725 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 967) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/967: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cc1nc[nH]n1) `ZINC001515213725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515213725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001515213725 none CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cc1nc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 5, 5, 5, 5, 3, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 19, 19, 19, 34, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 14, 19, 34, 34, 50] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213725 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001515213725 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213725/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213725/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213725 Building ZINC001515213970 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213970' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213970 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515213970 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213970/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213970 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/968 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CNC(C)=O) `ZINC001515213970.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515213970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001515213970 none CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CNC(C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 9, 24, 24, 24, 49, 50, 50, 50, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 24, 49, 49, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 197 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213970 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213970/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213970 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 969) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/969 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/969' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CNC(C)=O) `ZINC001515213970.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515213970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213970/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001515213970 none CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CNC(C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 21, 21, 21, 47, 50, 50, 50, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 11, 21, 47, 47, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213970 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001515213970 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213970/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213970/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213970 Building ZINC001515213970 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213970' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213970 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515213970 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213970/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213970 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 968) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/968: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CNC(C)=O) `ZINC001515213970.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515213970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001515213970 none CCO[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CNC(C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 9, 24, 24, 24, 49, 50, 50, 50, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 24, 49, 49, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 197 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213970 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213970/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213970 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 969) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/969: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CNC(C)=O) `ZINC001515213970.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515213970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213970/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001515213970 none CCO[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)CNC(C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 21, 21, 21, 47, 50, 50, 50, 5, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 11, 21, 47, 47, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213970 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001515213970 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213970/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213970/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515213970 Building ZINC001515221537 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515221537' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515221537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515221537 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515221537/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515221537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/970 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)CNC(=O)OC)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001515221537.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515221537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515221537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001515221537 none CCO[C@@H]1CN(C(=O)CNC(=O)OC)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 8, 1, 11, 12, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 15, 15, 15, 15, 15, 15, 20, 20, 29, 37, 50, 50, 50, 15, 11, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 15, 15, 29, 29, 37, 50, 50, 50, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515221537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515221537/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515221537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 971) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/971 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/971' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)CNC(=O)OC)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001515221537.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515221537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515221537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001515221537 none CCO[C@@H]1CN(C(=O)CNC(=O)OC)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 8, 1, 11, 12, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 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] 0 hydrogens 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, 16, 16, 16, 16, 16, 16, 20, 20, 30, 39, 50, 50, 50, 16, 9, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 16, 16, 30, 30, 39, 50, 50, 50, 16, 16, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515221537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001515221537 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515221537/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515221537/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515221537 Building ZINC001515221537 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515221537' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515221537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515221537 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515221537/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515221537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 970) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/970: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)CNC(=O)OC)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001515221537.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515221537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515221537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001515221537 none CCO[C@@H]1CN(C(=O)CNC(=O)OC)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 8, 1, 11, 12, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 15, 15, 15, 15, 15, 15, 20, 20, 29, 37, 50, 50, 50, 15, 11, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 15, 15, 29, 29, 37, 50, 50, 50, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515221537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515221537/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515221537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 971) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/971: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)CNC(=O)OC)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001515221537.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515221537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515221537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001515221537 none CCO[C@@H]1CN(C(=O)CNC(=O)OC)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 8, 1, 11, 12, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 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] 0 hydrogens 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, 16, 16, 16, 16, 16, 16, 20, 20, 30, 39, 50, 50, 50, 16, 9, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 16, 16, 30, 30, 39, 50, 50, 50, 16, 16, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [54, 46, 47, 48, 49, 50, 51, 20, 53, 22, 23, 24, 25, 26, 27, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515221537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001515221537 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515221537/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515221537/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515221537 Building ZINC001515229282 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515229282' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515229282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515229282 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515229282/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515229282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/972 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@H](C)NC(N)=O)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001515229282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515229282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515229282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001515229282 none CCO[C@@H]1CN(C(=O)[C@H](C)NC(N)=O)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 8, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 26, 26, 26, 26, 26, 26, 34, 34, 50, 50, 50, 50, 50, 50, 26, 16, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 26, 26, 50, 50, 50, 50, 50, 50, 26, 26, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [55, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 207 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515229282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515229282/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515229282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 973) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/973 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/973' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@H](C)NC(N)=O)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001515229282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515229282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515229282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001515229282 none CCO[C@@H]1CN(C(=O)[C@H](C)NC(N)=O)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 8, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 28, 28, 28, 28, 28, 28, 35, 35, 50, 50, 50, 50, 50, 50, 28, 14, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 28, 28, 50, 50, 50, 50, 50, 50, 28, 28, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [55, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515229282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001515229282 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515229282/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515229282/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515229282 Building ZINC001515229282 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515229282' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515229282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515229282 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515229282/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515229282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 972) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/972: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@H](C)NC(N)=O)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001515229282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515229282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515229282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001515229282 none CCO[C@@H]1CN(C(=O)[C@H](C)NC(N)=O)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 8, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 26, 26, 26, 26, 26, 26, 34, 34, 50, 50, 50, 50, 50, 50, 26, 16, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 26, 26, 50, 50, 50, 50, 50, 50, 26, 26, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [55, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 207 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515229282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515229282/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515229282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 973) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/973: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1CN(C(=O)[C@H](C)NC(N)=O)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001515229282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515229282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515229282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001515229282 none CCO[C@@H]1CN(C(=O)[C@H](C)NC(N)=O)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 7, 5, 8, 1, 8, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 28, 28, 28, 28, 28, 28, 35, 35, 50, 50, 50, 50, 50, 50, 28, 14, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 28, 28, 50, 50, 50, 50, 50, 50, 28, 28, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [55, 47, 48, 49, 50, 51, 52, 21, 54, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515229282 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001515229282 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515229282/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515229282/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001515229282 Building ZINC001520241576 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520241576' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520241576 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520241576 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520241576/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520241576 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/974 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]2C1) `ZINC001520241576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520241576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520241576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001520241576 none CNC(=O)NCC(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 50, 30, 12, 5, 12, 5, 5, 5, 5, 5, 5, 2, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 50, 50, 50, 50, 44, 30, 30, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 178 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520241576 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520241576/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520241576 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 975) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/975 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/975' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]2C1) `ZINC001520241576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520241576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520241576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001520241576 none CNC(=O)NCC(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 32, 11, 7, 11, 7, 7, 7, 7, 7, 6, 2, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50, 50, 47, 32, 32, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520241576 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001520241576 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520241576/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520241576/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520241576 Building ZINC001520241576 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520241576' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520241576 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520241576 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520241576/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520241576 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 974) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/974: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]2C1) `ZINC001520241576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520241576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520241576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001520241576 none CNC(=O)NCC(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 50, 30, 12, 5, 12, 5, 5, 5, 5, 5, 5, 2, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 50, 50, 50, 50, 44, 30, 30, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 178 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520241576 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520241576/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520241576 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 975) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/975: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]2C1) `ZINC001520241576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520241576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520241576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001520241576 none CNC(=O)NCC(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 32, 11, 7, 11, 7, 7, 7, 7, 7, 6, 2, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50, 50, 47, 32, 32, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520241576 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001520241576 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520241576/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520241576/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520241576 Building ZINC001520354236 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520354236' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520354236 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520354236 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520354236/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520354236 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/976 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1C[C@H]1C(N)=O) `ZINC001520354236.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520354236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520354236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001520354236 none CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1C[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 12, 6, 5, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 38, 38, 39, 39, 39, 39, 39, 50, 50, 20, 20, 20, 20, 20, 19, 19, 6, 6, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 50, 50] 50 rigid atoms, others: [48, 45, 43, 9, 42, 11, 12, 13, 14, 15, 16, 49, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 186 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520354236 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520354236/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520354236 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 977) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/977 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/977' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1C[C@H]1C(N)=O) `ZINC001520354236.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520354236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520354236/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001520354236 none CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1C[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 24, 17, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 25, 41, 41, 45, 45, 45, 45, 45, 50, 50, 25, 25, 25, 25, 25, 24, 24, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 50, 50] 50 rigid atoms, others: [48, 45, 43, 9, 42, 11, 12, 13, 14, 15, 16, 49, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 181 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520354236 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001520354236 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520354236/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520354236/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520354236 Building ZINC001520354236 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520354236' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520354236 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520354236 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520354236/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520354236 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 976) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/976: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1C[C@H]1C(N)=O) `ZINC001520354236.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520354236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520354236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001520354236 none CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1C[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 12, 6, 5, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 38, 38, 39, 39, 39, 39, 39, 50, 50, 20, 20, 20, 20, 20, 19, 19, 6, 6, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 50, 50] 50 rigid atoms, others: [48, 45, 43, 9, 42, 11, 12, 13, 14, 15, 16, 49, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 186 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520354236 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520354236/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520354236 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 977) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/977: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1C[C@H]1C(N)=O) `ZINC001520354236.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520354236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520354236/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001520354236 none CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1C[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 24, 17, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 25, 41, 41, 45, 45, 45, 45, 45, 50, 50, 25, 25, 25, 25, 25, 24, 24, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 50, 50] 50 rigid atoms, others: [48, 45, 43, 9, 42, 11, 12, 13, 14, 15, 16, 49, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 181 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520354236 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001520354236 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520354236/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520354236/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520354236 Building ZINC001520600299 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520600299' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520600299 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520600299 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520600299/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520600299 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/978 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN1CC(=O)N(C)C1=O) `ZINC001520600299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520600299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520600299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001520600299 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN1CC(=O)N(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 1, 11, 8, 5, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 12, 12, 33, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520600299 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520600299/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520600299 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 979) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/979 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/979' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN1CC(=O)N(C)C1=O) `ZINC001520600299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520600299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520600299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001520600299 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN1CC(=O)N(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 1, 11, 8, 5, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 16, 16, 41, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 41, 41, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 165 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520600299 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001520600299 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520600299/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520600299/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520600299 Building ZINC001520600299 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520600299' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520600299 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520600299 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520600299/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520600299 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 978) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/978: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN1CC(=O)N(C)C1=O) `ZINC001520600299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520600299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520600299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001520600299 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN1CC(=O)N(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 1, 11, 8, 5, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 12, 12, 33, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520600299 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520600299/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520600299 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 979) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/979: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN1CC(=O)N(C)C1=O) `ZINC001520600299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520600299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520600299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001520600299 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN1CC(=O)N(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 1, 11, 8, 5, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 16, 16, 41, 50, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 41, 41, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 165 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520600299 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001520600299 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520600299/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520600299/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520600299 Building ZINC001520607510 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607510' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607510 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520607510 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607510/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607510 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/980 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CC(=O)NC(=O)N1) `ZINC001520607510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520607510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001520607510 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CC(=O)NC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 22, 35, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 137 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607510 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607510/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607510 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 981) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/981 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/981' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CC(=O)NC(=O)N1) `ZINC001520607510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520607510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001520607510 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CC(=O)NC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 25, 34, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 143 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607510 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001520607510 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607510/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607510/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607510 Building ZINC001520607510 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607510' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607510 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520607510 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607510/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607510 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 980) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/980: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CC(=O)NC(=O)N1) `ZINC001520607510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520607510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001520607510 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CC(=O)NC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 22, 35, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 137 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607510 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607510/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607510 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 981) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/981: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CC(=O)NC(=O)N1) `ZINC001520607510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520607510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001520607510 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)[C@@H]1CC(=O)NC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 25, 34, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 143 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607510 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001520607510 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607510/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607510/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607510 Building ZINC001520607524 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607524' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607524 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520607524 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607524/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607524 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/982 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCS(N)(=O)=O) `ZINC001520607524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520607524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001520607524 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCS(N)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 14, 8, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 13, 13, 28, 31, 35, 50, 50, 50, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 28, 28, 34, 34, 35, 35, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 237 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607524 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607524/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607524 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 983) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/983 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/983' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCS(N)(=O)=O) `ZINC001520607524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520607524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001520607524 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCS(N)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 14, 8, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 16, 16, 32, 34, 38, 50, 50, 50, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 32, 32, 37, 37, 38, 38, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 234 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607524 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001520607524 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607524/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607524/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607524 Building ZINC001520607524 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607524' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607524 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520607524 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607524/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607524 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 982) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/982: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCS(N)(=O)=O) `ZINC001520607524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520607524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001520607524 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCS(N)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 14, 8, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 13, 13, 28, 31, 35, 50, 50, 50, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 28, 28, 34, 34, 35, 35, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 237 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607524 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607524/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607524 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 983) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/983: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCS(N)(=O)=O) `ZINC001520607524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520607524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001520607524 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CCCS(N)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 14, 8, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 16, 16, 32, 34, 38, 50, 50, 50, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 32, 32, 37, 37, 38, 38, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 234 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607524 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001520607524 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607524/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607524/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607524 Building ZINC001520607831 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607831' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520607831 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607831/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/984 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN1C(=O)CNC1=O) `ZINC001520607831.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520607831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001520607831 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN1C(=O)CNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 8, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 17, 17, 26, 50, 50, 50, 50, 50, 50, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 26, 26, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 138 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607831/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 985) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/985 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/985' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN1C(=O)CNC1=O) `ZINC001520607831.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520607831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607831/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001520607831 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN1C(=O)CNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 8, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 17, 17, 29, 50, 50, 50, 50, 50, 50, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 29, 29, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001520607831 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607831/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607831/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607831 Building ZINC001520607831 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607831' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520607831 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607831/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 984) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/984: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN1C(=O)CNC1=O) `ZINC001520607831.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520607831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001520607831 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN1C(=O)CNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 8, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 17, 17, 26, 50, 50, 50, 50, 50, 50, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 26, 26, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 138 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607831/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 985) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/985: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN1C(=O)CNC1=O) `ZINC001520607831.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520607831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607831/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001520607831 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)CN1C(=O)CNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 8, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 17, 17, 29, 50, 50, 50, 50, 50, 50, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 29, 29, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607831 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001520607831 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607831/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607831/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607831 Building ZINC001520607842 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607842' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520607842 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607842/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/986 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cn1ncn(C)c1=O) `ZINC001520607842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520607842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001520607842 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cn1ncn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 8, 1, 8, 5, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 12, 12, 33, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 33, 33, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607842/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 987) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/987 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/987' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cn1ncn(C)c1=O) `ZINC001520607842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520607842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001520607842 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cn1ncn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 8, 1, 8, 5, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 17, 17, 38, 50, 50, 50, 50, 50, 50, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 38, 38, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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/323031/xbw-8058115.49/working/building/ZINC001520607842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001520607842 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607842/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607842/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607842 Building ZINC001520607842 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607842' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520607842 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607842/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 986) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/986: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cn1ncn(C)c1=O) `ZINC001520607842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520607842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001520607842 none C[C@@H]1[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cn1ncn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 8, 1, 8, 5, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 12, 12, 33, 50, 50, 50, 50, 50, 50, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 33, 33, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607842/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 987) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/987: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cn1ncn(C)c1=O) `ZINC001520607842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520607842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001520607842 none C[C@@H]1[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCN1C(=O)Cn1ncn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 8, 1, 8, 5, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 17, 17, 38, 50, 50, 50, 50, 50, 50, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 38, 38, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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/323031/xbw-8058115.49/working/building/ZINC001520607842 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001520607842 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607842/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607842/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607842 Building ZINC001520607895 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607895' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607895 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520607895 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607895/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607895 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/988 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NS(C)(=O)=O)C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001520607895.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520607895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001520607895 none C[C@H](NS(C)(=O)=O)C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 5, 11, 11, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 20, 40, 40, 49, 50, 50, 50, 14, 20, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 40, 40, 40, 49, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607895 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607895/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607895 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 989) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/989 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/989' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NS(C)(=O)=O)C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001520607895.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520607895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607895/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001520607895 none C[C@H](NS(C)(=O)=O)C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 5, 11, 11, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 23, 39, 39, 50, 50, 50, 50, 13, 23, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 39, 39, 39, 50, 50, 50, 50, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 195 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607895 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001520607895 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607895/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607895/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607895 Building ZINC001520607895 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607895' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607895 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520607895 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607895/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607895 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 988) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/988: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NS(C)(=O)=O)C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001520607895.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520607895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001520607895 none C[C@H](NS(C)(=O)=O)C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 5, 11, 11, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 20, 40, 40, 49, 50, 50, 50, 14, 20, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 14, 14, 40, 40, 40, 49, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607895 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607895/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607895 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 989) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/989: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NS(C)(=O)=O)C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001520607895.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520607895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607895/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001520607895 none C[C@H](NS(C)(=O)=O)C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 5, 11, 11, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 23, 39, 39, 50, 50, 50, 50, 13, 23, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 39, 39, 39, 50, 50, 50, 50, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 195 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607895 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001520607895 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607895/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607895/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607895 Building ZINC001520607898 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607898' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607898 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520607898 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607898/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607898 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/990 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NS(C)(=O)=O)C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001520607898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520607898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001520607898 none C[C@@H](NS(C)(=O)=O)C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 5, 11, 11, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 19, 32, 32, 46, 50, 50, 50, 12, 19, 12, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 32, 32, 32, 46, 50, 50, 50, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607898 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607898/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607898 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 991) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/991 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/991' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NS(C)(=O)=O)C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001520607898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520607898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001520607898 none C[C@@H](NS(C)(=O)=O)C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 5, 11, 11, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 23, 35, 35, 47, 50, 50, 50, 13, 23, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 35, 35, 35, 47, 50, 50, 50, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 191 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607898 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001520607898 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607898/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607898/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607898 Building ZINC001520607898 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607898' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607898 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520607898 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607898/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607898 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 990) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/990: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NS(C)(=O)=O)C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001520607898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520607898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001520607898 none C[C@@H](NS(C)(=O)=O)C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 5, 11, 11, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 19, 32, 32, 46, 50, 50, 50, 12, 19, 12, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 32, 32, 32, 46, 50, 50, 50, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607898 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607898/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607898 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 991) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/991: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NS(C)(=O)=O)C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C) `ZINC001520607898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520607898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001520607898 none C[C@@H](NS(C)(=O)=O)C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 5, 11, 11, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 23, 35, 35, 47, 50, 50, 50, 13, 23, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 35, 35, 35, 47, 50, 50, 50, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 191 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607898 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001520607898 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607898/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607898/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520607898 Building ZINC001520710716 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520710716' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520710716 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520710716 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520710716/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520710716 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/992 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)CCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1C) `ZINC001520710716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520710716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520710716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001520710716 none CNS(=O)(=O)CCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 50, 50, 48, 23, 23, 23, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 49, 49, 48, 48, 23, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520710716 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520710716/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520710716 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 993) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/993 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/993' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)CCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1C) `ZINC001520710716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520710716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520710716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001520710716 none CNS(=O)(=O)CCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 50, 40, 12, 12, 12, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 42, 42, 40, 40, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520710716 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001520710716 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520710716/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520710716/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520710716 Building ZINC001520710716 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520710716' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520710716 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520710716 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520710716/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520710716 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 992) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/992: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)CCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1C) `ZINC001520710716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520710716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520710716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001520710716 none CNS(=O)(=O)CCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 50, 50, 48, 23, 23, 23, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 49, 49, 48, 48, 23, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520710716 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520710716/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520710716 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 993) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/993: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)CCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1C) `ZINC001520710716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520710716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520710716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001520710716 none CNS(=O)(=O)CCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 50, 40, 12, 12, 12, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 42, 42, 40, 40, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520710716 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001520710716 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520710716/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520710716/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001520710716 Building ZINC001521846316 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521846316' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521846316 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521846316 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521846316/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521846316 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/994 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CN2CC(=O)NC2=O)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001521846316.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521846316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521846316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001521846316 none C[C@@H]1CN(C(=O)CN2CC(=O)NC2=O)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 5, 1, 11, 8, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 50, 50, 50, 50, 50, 50, 28, 13, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 45, 45, 50, 50, 50, 28, 28, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521846316 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521846316/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521846316 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 995) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/995 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/995' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CN2CC(=O)NC2=O)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001521846316.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521846316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521846316/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001521846316 none C[C@@H]1CN(C(=O)CN2CC(=O)NC2=O)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 5, 1, 11, 8, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 43, 50, 50, 50, 50, 50, 50, 26, 16, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 43, 43, 50, 50, 50, 26, 26, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521846316 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001521846316 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521846316/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521846316/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521846316 Building ZINC001521846316 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521846316' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521846316 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521846316 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521846316/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521846316 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 994) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/994: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CN2CC(=O)NC2=O)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001521846316.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521846316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521846316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001521846316 none C[C@@H]1CN(C(=O)CN2CC(=O)NC2=O)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 5, 1, 11, 8, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 50, 50, 50, 50, 50, 50, 28, 13, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 45, 45, 50, 50, 50, 28, 28, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521846316 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521846316/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521846316 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 995) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/995: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)CN2CC(=O)NC2=O)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001521846316.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521846316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521846316/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001521846316 none C[C@@H]1CN(C(=O)CN2CC(=O)NC2=O)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 5, 1, 11, 8, 1, 11, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 43, 50, 50, 50, 50, 50, 50, 26, 16, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 43, 43, 50, 50, 50, 26, 26, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521846316 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001521846316 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521846316/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521846316/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521846316 Building ZINC001521847537 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521847537' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521847537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521847537 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521847537/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521847537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/996 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)Cn2c(O)nnc2O)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001521847537.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521847537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521847537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001521847537 none C[C@@H]1CN(C(=O)Cn2c(O)nnc2O)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'O.3', 'N.2', 'N.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 12, 8, 8, 1, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 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] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 27, 27, 28, 28, 49, 50, 50, 50, 50, 50, 50, 27, 15, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 49, 49, 150, 150, 27, 27, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 450 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 480 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521847537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521847537/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521847537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 997) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/997 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/997' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)Cn2c(O)nnc2O)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001521847537.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521847537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521847537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001521847537 none C[C@@H]1CN(C(=O)Cn2c(O)nnc2O)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'O.3', 'N.2', 'N.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 12, 8, 8, 1, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 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] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 33, 33, 34, 34, 47, 50, 50, 50, 50, 50, 50, 33, 21, 33, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 47, 47, 150, 150, 33, 33, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 450 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 464 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521847537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001521847537 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521847537/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521847537/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521847537 Building ZINC001521847537 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521847537' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521847537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521847537 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521847537/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521847537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 996) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/996: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)Cn2c(O)nnc2O)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001521847537.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521847537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521847537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001521847537 none C[C@@H]1CN(C(=O)Cn2c(O)nnc2O)C[C@H]1CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'O.3', 'N.2', 'N.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 12, 8, 8, 1, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 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] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 27, 27, 28, 28, 49, 50, 50, 50, 50, 50, 50, 27, 15, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 49, 49, 150, 150, 27, 27, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 450 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 480 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521847537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521847537/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521847537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 997) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/997: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)Cn2c(O)nnc2O)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001521847537.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521847537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521847537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001521847537 none C[C@@H]1CN(C(=O)Cn2c(O)nnc2O)C[C@H]1CNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'O.3', 'N.2', 'N.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 12, 8, 8, 1, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 4, 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] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 33, 33, 34, 34, 47, 50, 50, 50, 50, 50, 50, 33, 21, 33, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 47, 47, 150, 150, 33, 33, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 450 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 464 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521847537 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001521847537 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521847537/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521847537/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521847537 Building ZINC001521921341 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521921341' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521921341 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521921341 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521921341/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521921341 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/998 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1ncn(C)c1=O) `ZINC001521921341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521921341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521921341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001521921341 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1ncn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 14, 29, 29, 29, 45, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 14, 29, 45, 45, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521921341 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521921341/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521921341 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 999) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/999 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/999' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1ncn(C)c1=O) `ZINC001521921341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521921341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521921341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001521921341 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1ncn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 14, 24, 24, 24, 45, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 14, 14, 24, 45, 45, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521921341 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001521921341 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521921341/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521921341/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521921341 Building ZINC001521921341 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521921341' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521921341 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521921341 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521921341/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521921341 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 998) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/998: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1ncn(C)c1=O) `ZINC001521921341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521921341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521921341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001521921341 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1ncn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 1, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 14, 29, 29, 29, 45, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 14, 29, 45, 45, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521921341 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 mkdir: created directory `1' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521921341/1 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521921341 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 1 (index: 999) grep: /scratch/xiaobo/323031/xbw-8058115.49/working/3D/999: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1ncn(C)c1=O) `ZINC001521921341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521921341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521921341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001521921341 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)Cn1ncn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 14, 24, 24, 24, 45, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 14, 14, 24, 45, 45, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521921341 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001521921341 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 1: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521921341/1.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521921341/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521921341 Building ZINC001521928361 mkdir: created directory `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521928361' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521928361 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC001521928361 mkdir: created directory `0' /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521928361/0 /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521928361 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/xiaobo/323031/xbw-8058115.49/working/3D/1000 `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)C[C@H]1CC(=O)NC1=O) `ZINC001521928361.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521928361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521928361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001521928361 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]1CNC(=O)C[C@H]1CC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 14, 14, 14, 46, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 46, 46, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44] set([51, 50, 49, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 52]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521928361 /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Finished preparing ZINC001521928361 Recording results /scratch/xiaobo/323031/xbw-8058115.49/working /scratch/xiaobo/323031/xbw-8058115.49 Appending to /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.* 0: /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521928361/0.* Removing working files in /scratch/xiaobo/323031/xbw-8058115.49/working/building/ZINC001521928361 /scratch/xiaobo/323031/xbw-8058115.49 Compressing combined databse files /scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.db2.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/xiaobo/323031/xbw-8058115.49/finished) ======================================================= Finalizing... removed `/scratch/xiaobo/323031/xbw-8058115.49/working/3D/1001' removed directory: `/scratch/xiaobo/323031/xbw-8058115.49/working/3D' rmdir: removing directory, `/scratch/xiaobo/323031/xbw-8058115.49/working/building' rmdir: removing directory, `/scratch/xiaobo/323031/xbw-8058115.49/working' /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/logs `/scratch/xiaobo/323031/xbw-8058115.49' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xbw' `/scratch/xiaobo/323031/xbw-8058115.49/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xbw/finished' `/scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xbw/finished/xbw.db2.gz' removed `/scratch/xiaobo/323031/xbw-8058115.49/finished/xbw.db2.gz' removed directory: `/scratch/xiaobo/323031/xbw-8058115.49/finished' removed directory: `/scratch/xiaobo/323031/xbw-8058115.49'